Novel fungal enzymes

ABSTRACT

This invention relates to novel enzymes and novel methods for producing the same. More specifically this invention relates to a variety of fungal enzymes. Nucleic acid molecules encoding such enzymes, compositions, recombinant and genetically modified host cells, and methods of use are described. The invention also relates to a method to convert lignocellulosic biomass to fermentable sugars with enzymes that degrade the lignocellulosic material and novel combinations of enzymes, including those that provide a synergistic release of sugars from plant biomass. The invention also relates to methods to use the novel enzymes and compositions of such enzymes in a variety of other processes, including washing of clothing, detergent processes, deinking and biobleaching of paper and pulp, and treatment of waste streams.

REFERENCE TO SEQUENCE LISTING

This application contains a Sequence Listing submitted as an electronic text file named “5671-5_ST25.txt”, having a size in bytes of 366 kb, and created on 2 Aug. 2007, the information contained in this electronic file is hereby incorporated by reference in its entirety pursuant to 37 CFR §1.52(e)(5).

FIELD OF THE INVENTION

This invention relates to novel enzymes and novel methods for producing the same. More specifically this invention relates to enzymes produced by fungi. The invention also relates to a method to convert lignocellulosic biomass to fermentable sugars with enzymes that degrade the lignocellulosic material and novel combinations of enzymes, including those that provide a synergistic release of sugars from plant biomass. The invention also relates to methods to use the novel enzymes and compositions of such enzymes in a variety of other processes, including washing of clothing, detergent processes, deinking and biobleaching of paper and pulp, and treatment of waste streams.

BACKGROUND OF THE INVENTION

Large amounts of carbohydrates in plant biomass provide a plentiful source of potential energy in the form of sugars (both five carbon and six carbon sugars) that can be utilized for numerous industrial and agricultural processes. However, the enormous energy potential of these carbohydrates is currently under-utilized because the sugars are locked in complex polymers, and hence are not readily accessible for fermentation. These complex polymers are often referred to collectively as lignocellulose. Sugars generated from degradation of plant biomass potentially respresent plentiful, economically competitive feedstocks for fermentation into chemicals, plastics, and fuels, including ethanol as a substitute for petroleum.

For example, distillers' dried grains (DDG) are lignocellulosic byproducts of the corn dry milling process. Milled whole corn kernels are treated with amylases to liquefy the starch within the kernels and hydrolyze it to glucose. The glucose so produced is then fermented in a second step to ethanol. The residual solids after the ethanol fermentation and distillation are centrifuged and dried, and the resulting product is DDG, which is used as an animal feed stock. Although DDG composition can vary, a typical composition for DDG is: 32% hemicellulose, 22% cellulose, 30% protein, 10% lipids, 4% residual starch, and 4% inorganics. In theory, the cellulose and hemicellulose fractions, comprising about 54% of the weight of the DDG, can be efficiently hydrolyzed to fermentable sugars by enzymes; however, it has been found that the carbohydrates comprising lignocellulosic materials in DDG are more difficult to digest. To date, the efficiency of hydrolysis of these (hemi) cellulosic polymers by enzymes is much lower than the hydrolytic efficiency of starch, due to the more complex and recalcitrant nature of these substrates. Accordingly, the cost of producing, the requisite enzymes is higher than the cost of producing amylases for starch hydrolysis.

Major polysaccharides comprising lignocellulosic materials include cellulose and hemicelluloses. The enzymatic hydrolysis of these polysaccharides to soluble sugars (and finally to monomers such as glucose, xylose and other hexoses and pentoses) is catalyzed by several enzymes acting in concert. For example, endo-1,4-β-glucanases (EGs) and exo-cellobiohydrolases (CBHs) catalyze the hydrolysis of insoluble cellulose to cellooligosachharides (with cellobiose the main product), while β-glucosidaes (BGLs) convert the oligosaccharides to glucose. Similarly, xylanases, together with other enzymes such as α-L-arabinofuranosidases, feruloyl and acetylxylan esterases and β-xylosidases, catalyze the hydrolysis of hemicelluloses.

Regardless of the type of cellulosic feedstock, the cost and hydrolytic efficiency of enzymes are major factors that restrict the widespread use of biomass bioconversion processes. The hydrolytic efficiency of a multi-enzyme complex in the process of lignocellulosic saccharification depends both on properties of the individual enzymes and the ratio of each enzyme within the complex.

Enzymes useful for the hydrolysis of complex polysaccharides are also highly useful in a variety of industrial textile applications, as well as industrial paper and pulp applications, and in the treatment of waste streams. For example, as an alternative to the use of pumice in the stone washing process, methods for treating cellulose-containing fabrics for clothing with hydrolytic enzymes, such as cellulases, are known to improve the softness or feel of such fabrics. Cellulases are also used in detergent compositions, either for the purpose of enhancing the cleaning ability of the composition or as a softening agent. Cellulases are also used in combination with polymeric agents in processes for providing a localized variation in the color density of fibers. Such enzymes can also be used for the saccharification of lignocellulosic biomass in waste streams, such as municipal solid waste, for biobleaching of wood pulp, and for deinking of recycled print paper. As with the hydrolysis of these polysaccharides in lignocellulosic materials for use as feedstocks described above, the cost and hydrolytic efficiency of the enzymes are major factors that control the use of enzymes in these processes.

Filamentous fungi are a source of cellulases and hemicellulases, as well as other enzymes useful in the enzymatic hydrolysis of major polysaccharides. In particular, strains of Trichoderma sp., such as T. viride, T. reesei and T. longibrachiatum, and Penicillium sp., and enzymes derived from these strains, have previously been used to hydrolyze crystalline cellulose. However, the costs associated with producing enzymes from these fungi, as well as the presence of additional, undesirable enzymes, remains a drawback. It is therefore desirable to produce inexpensive enzymes and enzyme mixtures that efficiently degrade cellulose and hemicellulose for use in a variety of agricultural and industrial applications.

SUMMARY OF THE INVENTION

The present invention provides isolated nucleic acid molecules comprising a nucleic acid sequence selected from the group consisting of:

-   -   a) a nucleic acid sequence encoding a protein comprising an         amino acid sequence selected from the group consisting of: SEQ         ID NO:11, SEQ ID NO:23, SEQ ID NO:29, SEQ ID NO:32, SEQ ID         NO:35, SEQ ID NO:38, SEQ ID NO:41, SEQ ID NO:44, SEQ ID NO:50,         SEQ ID NO:53, SEQ ID NO:56, SEQ ID NO:59, SEQ ID NO:62, SEQ ID         NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77,         SEQ ID NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, SEQ ID         NO:92, and SEQ ID NO:94.     -   b) a nucleic acid sequence encoding a fragment of the protein of         (a), wherein the fragment has a biological activity of the         protein of (a); and     -   c) a nucleic acid sequence encoding an amino acid sequence that         is at least 70% identical to an amino acid sequence of (a) and         has a biological activity of the protein comprising the amino         acid sequence.

In some embodiments, the nucleic acid sequence encodes an amino acid sequence that is at least 90%, at least 95%, at least 97%, or at least 99% identical to the amino acid sequence of (a) and has a biological activity of the protein comprising the amino acid sequence.

In some embodiments, the nucleic acid sequence encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ NO:11, SEQ ID NO:23, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38, SEQ ID NO:41, SEQ ID NO:44, SEQ ID NO:50, SEQ ID NO:53, SEQ ID NO:56, SEQ ID NO:59, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77, SEQ ID NO:80, SEQ ID NO. 3, SEQ ID NO:86, SEQ ID NO:89, SEQ ID NO:92, and SEQ ID NO:94.

In some embodiments, the nucleic acid sequence consists of a nucleic acid sequence selected from the group consisting of: SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:79, SEQ ID NO:90, SEQ ID NO:91 and SEQ ID NO:93.

In some embodiments, the nucleic acid sequence encodes a protein comprising the ammo acid sequence of SEQ ID NO:11, wherein the protein has cellobiohydrolase activity.

In some embodiments, the nucleic acid sequence encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:94 and SEQ ID NO:23, wherein the protein has endoglucanase activity.

In some embodiments, the nucleic acid sequence encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38 and SEQ ID NO:41, wherein the protein has xylanase activity.

In some embodiments, the nucleic acid sequence encodes a protein comprising an amino acid sequence of SEQ ID NO:44, wherein the protein has β-glucosidase activity.

In some embodiments, the nucleic acid sequence encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:50, SEQ ID NO:53, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77, SEQ ID NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, and SEQ ID NO:92, wherein the protein has hemicellulase activity.

In some embodiments, the nucleic acid sequence encodes a protein comprising the amino acid sequence of SEQ ID NO:50, wherein the protein has glucoamylase activity.

In some embodiments, the nucleic acid sequence encodes a protein comprising the amino acid sequence of SEQ ID NO:53, wherein the protein has pectate lyase activity.

In some embodiments, the nucleic acid sequence encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:56 and SEQ ID NO:59, wherein the protein has chitinase activity.

In some embodiments, the nucleic acid sequence encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:62, SEQ ID NO:80, and SEQ ID NO:83, wherein the protein has acetylxylan esterase activity.

In some embodiments, the nucleic acid sequence encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:65, SEQ ID NO:68, and SEQ ID NO:71, wherein the protein has ferulic acid esterase activity.

In some embodiments, the nucleic acid sequence encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:74 and SEQ ID NO:77, wherein the protein has arabinofuranosidase activity.

In some embodiments, the nucleic acid sequence encodes a protein comprising the amino acid sequence of SEQ ID NO:86, wherein the protein has pectin methyl esterase activity.

In some embodiments, the nucleic acid sequence of (a) encodes a protein comprising the amino acid sequence of SEQ ID NO:89, wherein the protein has endo-arabinase activity.

In some embodiments, the nucleic acid sequence encodes a protein comprising the amino acid sequence of SEQ ID NO:92, wherein the protein has β-xylosidase or β-glucosidaseactivity.

In some embodiments, the nucleic acid sequence encoding a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:2 and SEQ ID NO:5.

In some embodiments, the nucleic acid sequence is fully complementary to any of the nucleic acid sequences described above.

The invention also provides a protein comprising an amino acid sequence encoded by the nucleic acid molecules of the present invention.

In some embodiments, the protein comprises an amino acid sequence selected from the group consisting of: SEQ ID NO:11, SEQ ID NO:23, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38, SEQ ID NO:41, SEQ ID NO:44, SEQ ID NO:50, SEQ ID NO:53, SEQ ID NO:56, SEQ ID NO:59, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77, SEQ ID NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, SEQ ID NO:92, and SEQ ID NO:94.

In some embodiments, the protein comprises an amino acid sequence selected from SEQ ID NO:56 and SEQ ID NO:59, wherein the protein has chitinase activity.

The invention also provides an isolated fusion protein comprising an isolated protein of the present invention fused to a protein comprising an amino acid sequence that is heterologous to the isolated protein of the present invention.

The invention also provides an isolated antibody or antigen binding fragment thereof that selectively binds to a protein of the present invention.

The invention also provides a kit for degrading a lignocellulosic material to fermentable sugars comprising at least one isolated protein of the present invention.

The invention also provides a detergent comprising at least one isolated protein of the present invention

The invention also provides a composition for the degradation of a lignocellulosic material comprising at least one isolated protein of the present invention.

The invention also provides a recombinant nucleic acid molecule comprising an isolated nucleic acid molecule of the present invention, operatively linked to at least one expression control sequence.

In some embodiments, the recombinant nucleic acid molecule comprises an expression vector. In some embodiments, the recombinant nucleic acid molecule comprises a targeting vector.

The invention also provides an isolated host cell transfected with a nucleic acid molecule of the present invention.

In some embodiments, the host cell is a fungus. In some embodiments, the host cell is a filamentous fungus. In some embodiments, the filamentous fungus is from a genus selected from the group consisting of: Chrysosporium, Thielavia, Neurospora, Aureobasidium, Filibasidium, Piromyces, Corynascus, Coplococcus, Acremonium, Tolypocladium, Scytalidium, Schizophyllum, Sporotrichum, Penicillium, Gibberella, Myceliophthora, Mucor, Aspergillus, Fusarium, Hunicola, and Trichoderma, and anamorphs and teleomorphs thereof. In some embodiments, the host cell is a bacterium.

The invention also provides an oligonucleotide consisting essentially of at least 12 consecutive nucleotides of a nucleic acid sequence selected from the group consisting of: SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:79, SEQ ID NO:90, SEQ ID NO:91, and SEQ ID NO:93, or the complement thereof.

The invention also provides a kit comprising at least one oligonucleotide of the present invention.

The invention also provides a method for producing a protein of the present invention, comprising culturing a cell that has been transfected with a nucleic acid molecule comprising a nucleic acid sequence encoding the protein, and expressing the protein with the transfected cell.

In some embodiments, the method further comprises recovering the protein from the cell or from a culture comprising the cell.

The invention also provides a genetically modified organism comprising components suitable for degrading a lignocellulosic material to fermentable sugars, wherein the organism has been genetically modified to express at least one protein of the present invention.

In some embodiments, the genetically modified organism is a microorganism. In some embodiments, the microorganism is a filamentous fungus.

In some embodiments, the filamentous fungus is from a genus selected from the group consisting of: Chrysosporium, Thielavia, Neurospora, Aureobasidium, Filibasidium, Piromyces, Corynascus, Cryplococcus, Acremonium, Tolypocladium, Scytalidium, Schizophyllum, Sporotrichum, Penicillium, Talaromyces, Gibberella, Myceliophthora, Mucor, Aspergillus, Fusarium, Humicola, and Trichoderma.

In some embodiments, the filamentous fungus is selected from the group consisting of: Trichoderma reesei, Chlysosporium lucknowense, Aspergillus japonicus, Penicillium canescens, Penicillium solitum, Penicillium funiculosum, and Talaromyces flavus.

In some embodiments, the organism has been genetically modified to express at least one additional enzyme.

In some embodiments, the additional enzyme is an accessory enzyme selected from the group consisting of: cellulase, xylanase, ligninase, glucuronidase, arabinofuranosidase, arabinogalactanase, ferulic acid esterase, lipase, pectinase, glucomannase, amylase, laminarinase, xyloglucanase, galactanase, glucoamylase, pectate lyase, chitinase, exo-•-D-glucosaminidase, cellobiose dehydrogenase, and acetylxylan esterase.

In some embodiments, the genetically modified organism is a plant.

The invention also provides a recombinant enzyme isolated from a genetically modified microorganism of the present invention.

In some embodiments, the enzyme has been subjected to a purification step.

The invention also provides a crude fermentation product produced by culturing the comprising a genetically modified microorganism of the present invention, wherein the crude fermentation product contains at least one protein of the present invention.

The invention also provides a multi-enzyme composition comprising enzymes produced by a genetically modified organism of the present invention and recovered therefrom.

The invention also provides a multi-enzyme composition comprising at least one protein of the present invention and at least one additional protein for degrading a lignocellulosic material or a fragment thereof that has biological activity.

In some embodiments, the at least one additional protein for degrading a lignocellulosic material to fermentable sugars is selected from the group consisting of: SEQ ID NO:8, SEQ ID NO:14, SEQ ID NO:17, SEQ ID NO:20, SEQ ID NO:26 and SEQ ID NO:47, or a fragment thereof that has biological activity.

In some embodiments, the multi-enzyme composition comprises at least one cellobiohydrolase, at least one xylanase, at least one endoglucanase, at least one •-glucosidase, at least one •-xylosidase, and at least one accessory enzyme.

In some embodiments, between about 50% and about 70% of the enzymes in the composition are cellobiohydrolases.

In some embodiments, between about 10% and about 30% of the enzymes in the composition are xylanases.

In some embodiments, between about 5% and about 15% of the enzymes in the composition are endoglucanases.

In some embodiments, between about 1% and about 5% of the enzymes in the composition are •-glucosidases.

In some embodiments, between about 1% and about 3% of the enzymes in the composition are •-xylosidases.

In some embodiments, the composition comprises about 60% cellobiohydrolases, about 20% xylanases, about 10% endoglucanases, about 3% •-glucosidases, about 2% •-xylosidases, and about 5% accessory enzymes.

In some embodiments, the xylanases are selected from the group consisting of: endoxylanases, exoxylanases, and •-xylosidases.

In some embodiments, the accessory enzymes include an enzyme selected from the group consisting of: ligninase, glucuronidase, arabinofuranosidase, arabinogalactanase, furilic acid esterase, lipase, pectinase, glucomannase, amylase, laminarinase, xyloglucanase, galactanase, glucoamylase, pectate lyase, chitinase, exo-•-D-glucosaminidase, cellobiose dehydrogenase, and acetylxylan esterase.

In some embodiments, the composition comprises at least one protein comprising the amino acid sequence of SEQ ID NO:11, wherein the protein has cellobiohydrolase activity, at least one protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:94 and SEQ ID NO:23, wherein the protein has endoglucanase activity, at least one protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38 and SEQ ID NO:41, wherein the protein has xylanase activity, at least one protein comprising an amino acid sequence of SEQ ID NO:44, wherein the protein has •-glucosidase activity, and at least one protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:50, SEQ ID NO:53, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ NO:74, SEQ ID NO:77, SEQ ID NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, and SEQ ID NO:92, wherein the protein has hemicellulase activity.

In some embodiments, the composition comprises at least one first protein comprising an amino acid sequence that is at least 95% identical to an amino acid sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8 and SEQ ID NO:11 and has cellobiohydrolase activity, or a fragment thereof that has cellobiohydrolase activity; at least one second protein comprising an amino acid sequence that is at least 95% identical to an amino acid sequence selected from the group consisting of: SEQ NO:14, SEQ ID NO:94, SEQ ID NO:17, SEQ ID NO:20 and SEQ ID NO:23 and has endoglucanase activity, or a fragment thereof that has endoglucanase activity; and at least one third protein comprising an amino acid sequence that is at least 95% identical to an amino acid sequence selected from the group consisting of: SEQ ID NO:26, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38 and SEQ ID NO:41 and has xylanase activity, or a fragment thereof that has xylanase activity.

In some embodiments, the composition further comprises a fourth protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:44 and has β-glucosidase activity, or a fragment thereof that has β-glucosidase activity.

In some embodiments, the composition further comprises at least one fifth protein comprising an amino acid sequence that is at least 95% identical to an amino acid sequence selected from the group consisting of: SEQ ID NO:47, SEQ ID NO:50, SEQ ID NO:53, SEQ ID NO:56, SEQ ID NO:59, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77, SEQ NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, and SEQ ID NO:92, and has hemicellulase or chitinase activity, or a fragment thereof that has hemicellulose or chitinase activity

The invention also provides a multi-enzyme composition comprising a first protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:2 and has cellobiohydrolase activity, or a fragment thereof that has cellobiohydrolase activity; a second protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:8 and has cellobiohydrolase activity, or a fragment thereof that has cellobiohydrolase activity; a third protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:94 and has endoglucanase activity, or a fragment thereof that has endoglucanase activity; a fourth protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:29 and has xylanase activity, or a fragment thereof that has xylanase activity; and a fifth protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:44 and has β-glucosidase activity, or a fragment thereof that has β-glucosidase activity.

In some embodiments, the multi-enzyme composition further comprises a sixth protein that has β-xylosidase activity, or a fragment thereof that has β-xylosidase activity.

In some embodiments, the multi-enzyme composition further comprises one or more proteins selected from the group consisting of:

-   -   a) a protein comprising an amino acid sequence that is at least         95% identical to SEQ ID NO:5 and has cellobiohydrolase activity,         or a fragment thereof that has cellobiohydrolase activity;     -   b) a protein comprising an amino acid sequence that is at least         95% identical to SEQ ID NO:20 and has endoglucanase activity, or         a fragment thereof that has endoglucanase activity;     -   c) a protein comprising an amino acid sequence that is at least         95% identical to SEQ ID NO:26 and has xylanase activity, or a         fragment thereof that has xylanase activity; and     -   d) a protein comprising an amino acid sequence that is at least         95% identical to SEQ ID NO:47 and has arabinogalactanase         activity, or a fragment thereof that has arabinogalactanase         activity.

In some embodiments, the multi-enzyme composition comprises at least one hemicellulase.

In some embodiments, the hemicellulase is selected from the group consisting of a xylanase, an arabinofuranosidase, an acetyl xylan esterase, a glucuronidase, and endo-galactanase, a mannanase, an endo arabinase, an exo arabinase, an exo-galactanase, a ferulic acid esterase, a galactomannanase, a xylogluconase, and mixtures thereof.

In some embodiments, the xylanase is selected from the group consisting of endoxylanases, exoxylanase, and β-xylosidase.

In some embodiments, the multi-enzyme composition comprises at least one cellulase.

In some embodiments, the composition is a crude fermentation product.

In some embodiments, the composition is a crude fermentation product that has been subjected to a purification step.

In some embodiments, the multi-enzyme composition further comprises one or more accessory enzymes.

In some embodiments, the accessory enzyme includes at least one enzyme selected from the group consisting of: cellulase, xylanase, ligninase, glucuronidase, arabinofuranosidase, arabinogalactanase, furilic acid esterase, lipase, pectinase, glucomannase, amylase, laminarinase, xyloglucanase, galactanase, glucoamylase, pectate lyase, chitinase, exo-•-D-glucosaminidase, cellobiose dehydrogenase, and acetylxylan esterase.

In some embodiments, the accessory enzyme is selected from the group consisting of a glucoamylase, a pectinase, and a ligninase.

In some embodiments, the accessory enzyme is a glucoamylase.

In some embodiments, the accessory enzyme is added as a crude or a semi-purified enzyme mixture.

In some embodiments, the accessory enzyme is produced by culturing at least one organism on a substrate to produce the enzyme.

The invention also provides a method for degrading a lignocellulosic material to fermentable sugars, comprising contacting the lignocellulosic material with at least one isolated protein of the present invention.

In some embodiments, the isolated protein is part of a multi-enzyme composition.

The invention also provides a method for degrading a lignocellulosic material to fermentable sugars, comprising contacting the lignocellulosic material with at least one multi-enzyme composition of the present invention.

The invention also provides a method for producing an organic substance, comprising:

-   -   a) saccharifying a lignocellulosic material with a multi-enzyme         composition of the present invention;     -   b) fermenting the saccharified lignocellulosic material obtained         with one or more fermentating microoganisms; and     -   c) recovering the organic substance from the fermentation.

In some embodiments, the steps of saccharifying and fermenting are performed simultaneously.

In some embodiments, the organic substance is an alcohol, organic acid, ketone, amino acid, or gas.

In some embodiments, the organic substance is an alcohol. In some embodiments, the alcohol is ethanol.

In some embodiments, the lignocellulosic material is selected from the group consisting of consisting of herbaceous material, agricultural residue, forestry residue, municipal solid waste, waste paper, and pulp and paper mill residue.

In some embodiments, the lignocellulosic material is distiller's dried grains or distiller's dried grains with solubles.

In some embodiments, the distiller's dried grains or distiller's dried grains with solubles is derived from corn.

The invention also provides a method for degrading a lignocellulosic material consisting of distiller's dried grains or distiller's dried grains with solubles to sugars, the method comprising contacting the distiller's dried grains or distiller's dried grains with solubles with a multi-enzyme composition, whereby at least 10% of the fermentable sugars are liberated, wherein the multi-enzyme composition is the multi-enzyme composition of the present invention.

In some embodiments, at least 15% of the sugars are liberated. In some embodiments, at least 20% of the sugars are liberated. In some embodiments, at least 23% of the sugars are liberated.

In some embodiments, the distiller's dried grains or distiller's dried grains with solubles is derived from corn.

In some embodiments, the method further comprises a pretreatment process for pretreating the lignocellulosic material.

In some embodiments, the pretreatment process is selected from the group consisting of physical treatment, metal ion, ultraviolet light, ozone, organosolv treatment, steam explosion treatment, lime impregnation with steam explosion treatment, hydrogen peroxide treatment, hydrogen peroxide/ozone (peroxone) treatment, acid treatment, dilute acid treatment, and base treatment.

In some embodiments, the pretreatment process is selected from the group consisting of organosolv, steam explosion, heat treatment and AFEX.

In some embodiments, the heat treatment comprises heating the lignocellulosic material to 121° C. for 15 minutes:

In some embodiments, the method further comprises detoxifying the lignocellulosic material.

In some embodiments, the method further comprises recovering the fermentable sugar.

In some embodiments, the sugar is selected from the group consisting of glucose, xylose, arabinose, galactose, mannose, rhamnose, sucrose and fructose.

In some embodiments, the method further comprises recovering the contacted lignocellulosic material after the fermentable sugars are degraded.

The invention also provides a feed additive comprising a recovered lignocellulosic material.

In some embodiments, the protein content of the recovered lignocellulosic material is higher than that of the starting lignocellulosic material.

The invention also provides a method of improving the performance of an animal which comprises administering to the animal a feed additive of the present invention.

The invention also provides a method for improving the nutritional quality of an animal feed comprising adding a feed additive of the present invention to an animal feed.

The invention also provides a method for stonewashing a fabric, comprising contacting the fabric with at least one isolated protein of the present invention.

The invention also provides a method for stonewashing a fabric, comprising contacting the fabric with at least one multi-enzyme composition of the present invention.

In some embodiments, the fabric is denim.

The invention also provides a method for enhanching the softness or feel of a fabric or depilling a fabric, comprising contacting the fabric with at least one isolated protein of the present invention or a fragment thereof comprising a cellulose binding domain (CBD) of the protein.

The invention also provides a method for enhanching the softness or feel of a fabric or depilling a fabric, comprising contacting the fabric with at least one multi-enzyme composition of the present invention.

The invention also provides a method for restoring color to or brightening a fabric, comprising contacting the fabric with at least one isolated protein of the present invention.

The invention also provides a method for restoring color to or brightening a fabric, comprising contacting the fabric with at least one multi-enzyme composition of the present invention.

The invention also provides a method of biopolishing, defibrillating, bleaching, dyeing or desizing a fabric, comprising contacting the fabric with at least one isolated protein of the present invention.

The invention also provides a method of biopolishing, defibrillating, bleaching, dyeing or desizing a fabric, comprising contacting the fabric with at least one multi-enzyme composition of the present invention.

The invention also provides a method of deinking or biobleaching paper or pulp, comprising contacting the paper or pulp with at least one isolated protein of the present invention.

The invention also provides a method of deinking or biobleaching paper or pulp, comprising contacting the paper or pulp with at least one multi-enzyme composition of the present invention.

The invention also provides a method for enhancing the cleaning ability of a detergent composition, comprising adding at least one isolated protein of the present invention to the detergent composition.

The invention also provides a method for enhancing the cleaning ability of a detergent composition, comprising adding at least one multi-enzyme composition of the present invention to the detergent composition.

The invention also provides a detergent composition, comprising at least one isolated protein of the present invention and at least one surfactant.

The invention also provides a detergent composition, comprising at least one multi-enzyme composition of the present invention and at least one surfactant.

The invention also provides a method for inhibiting or reducing fungal growth, comprising contacting a fungus or an area susceptible to fungal growth with at least one isolated protein comprising an amino acid sequence selected from the group consisting of SEQ ID NO:56 and SEQ ID NO:59, wherein the protein has chitinase activity.

The invention also provides a method for reducing or preventing insect infestation on a plant, comprising contacting the plant with at least one isolated protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:56 and SEQ ID NO:59, wherein the protein has chitinase activity.

The invention also provides a method for reducing or preventing allergic inflammation or asthma, comprising administering at least one isolated protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:56 and SEQ ID NO:59, wherein the protein has chitinase activity.

The invention also provides a lysing enzyme for the generation of protoplasts from fungi, comprising at least one isolated protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:56 and SEQ ID NO:59, wherein the protein has chitinase activity.

The invention also provides an insecticide composition, comprising at least one isolated protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:56 and SEQ ID NO:59, wherein the protein has chitinase activity.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows the specific activity of cellobiohydrolases and endoglucanases of the present invention toward the indicated substrates. Specific activities (Units/mg) were determined at pH 5.0 and 50° C.

FIG. 2 illustrates the enzymatic activity (percentage of maximum) of cellobiohydrolases of the present invention at varying pH levels. The activities were determined using an Avicel substrate at 40° C.

FIG. 3 illustrates the enzymatic activity (percentage of maximum) of cellobiohydrolases of the present invention at varying temperature levels. The activities were determined using an Avicel substrate at pH 5.0.

FIG. 4 illustrates the enzymatic activity (percentage of maximum) of endoglucanases of the present invention at varying pH levels. The activities were determined using an CMC substrate at 50° C.

FIG. 5 illustrates the enzymatic activity (percentage of maximum) of endoglucanases of the present invention at varying temperature levels. The activities were determined using a CMC substrate at pH 5.0.

FIG. 6 shows the specific activity of xylanases of the present invention toward the indicated substrates. Specific activities (Units/mg) were determined at pH 5.0 and 50° C.

FIG. 7 illustrates the enzymatic activity (percentage of maximum) of xylanases of the present invention at varying pH levels. The activities were determined using a soluble xylan substrate at 40° C.

FIG. 8 illustrates the enzymatic activity (percentage of maximum) of xylanases of the present invention at varying temperature levels. The activities were determined using a soluble xylan substrate at pH 5.0.

FIG. 9 illustrates the enzymatic activity (percentage of maximum) of enzymes of the present invention at varying pH levels.

FIG. 10 illustrates the enzymatic activity (percentage of maximum) of enzymes of the present invention at varying temperature levels.

FIG. 11 shows a standard calibration plot for the Somogyi-Nelson assay used for the measurement of reducing sugars in enzymatic hydrolyzates.

FIG. 12 shows a standard calibration plot with glucose standards from 0.025 g/l to 0.5 g/l for a glucosooxidase-peroxidase assay used to determine glucose levels.

FIG. 13 shows the relative activity over time of xylanase at 20-, 10- and 5-fold dilutions in a thermoshock assay.

FIG. 14 shows the pelletizing stability of xylanases of the present invention. The percentage of activity after 20 seconds at 80° C. relative to an unheated sample is shown.

FIG. 15 shows the relative viscosity of water/rye mixes treated with the indicated enzyme(s). To compare the efficiency of the preparations, the xylanase activities of the samples (units per flask) are also indicated.

FIG. 16 shows a plot of the residual viscosity (%) of water/rye mixes) after enzymatic treatment.

FIG. 17 shows a graph of the residual viscosity (%) of rye meal water extract after a 1-hour incubation with 1 unit of the indicated xylanase (in vitro feed test).

FIG. 18 shows the biobleaching ability (A₂₃₅) of xylanases of the present invention on soft wood pulp at pH 7.5 and 50° C. for 2 hours. For each xylanase, the assay was conducted using 0.01, 0.003, 0.001, 0.0003 mg/ml of enzyme in the reaction mixture, as indicated.

FIG. 19 shows the biobleaching ability (A₂₃₅) of xylanases of the present invention on hard wood pulp at pH 7.5 and 50° C. for 2 hours. For each xylanase, the assay was conducted using 0.01, 0.003, 0.001, 0.0003 mg/ml of enzyme in the reaction mixture, as indicated.

FIG. 20 illustrates the bioscouring ability of cellobiohydrolases and endoglucanases of the present invention. The reciprocal of the time (0.1/time; sec⁻¹) of water drop adsorption on a textile after treatment at pH 5.0 with 0.6 mg/l of enzyme followed by heating is shown. The water drop adsorption time for the untreated control sample is 2400 sec (l/time=0.0004).

FIG. 21 illustrates a comparison of the pectin content in an unscoured sample, an alkaline scoured sample, and bioscoured samples.

FIG. 22 shows a diagram of cells for the enzymatic and mechanical stress treatment of fabric. In FIG. 22A, the following numbers represent the indicated structure: 1: glass vessel, 2: plastic tube, 3: denim swatch, 4: rubber ring, 5: buckshot balls, and 6: teflon disk. In FIG. 22B, the following numbers represent the indicated structure: 1: lid with a thread inside, 2: rubber ring. 3: cell body (stainless steel), 4: cylindrical cartridge, 5: stainless steel cylinders, 6: circular denim swatch.

FIG. 23 illustrates the biopolishing ability of cellobiohydrolases and endoglucanases of the present invention. The dye release (D 400 nm) after treatment with 0.2 g/l enzyme at pH 5.0, 50° C. is shown.

FIG. 24 shows an example histogram generated from the color intensity analysis of a denim swatch.

FIG. 25 illustrates the denim-washing (abrasion) ability of cellobiohydrolases and endoglucanases of the present invention. The relative units per mg of enzyme determined at 50° C., pH 5.0 is shown.

FIG. 26 shows a graph of the saccharification ability of cellobiohydrolases and endoglucanases of the present invention. The amount of glucose (g/l) produced after the hydrolysis of 5 g/l Avicel at pH 5.0, 40° C. for 120 hours in the presence of 0.1 mg/ml enzyme and 0.2 U/ml cellobiase is shown.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates generally to proteins that play a role in the degradation of cellulose and hemicellulose and nucleic acids encoding the same. In particular, the present invention relates to enzymes isolated from a filamentous fungal strain denoted herein as C1 (Accession No. VKM F-3500-D), nucleic acids encoding the enzymes, and methods of producing and using the enzymes. The invention also provides compositions that include at least one of the enzymes described herein for uses including, but not limited to, the hydrolysis of lignocellulose. The invention stems, in part, from the discovery of a variety of novel cellulases and hemicellulases produced by the C1 fungus that exhibit high activity toward cellulose and other components of biomass.

The present invention also provides methods and compositions for the conversion of plant biomass to fermentable sugars that can be converted to useful products. The methods include methods for degrading lignocellulosic material using enzyme mixtures to liberate sugars. The compositions of the invention include enzyme combinations that break down lignocellulose. As used herein the terms “biomass” or “lignocellulosic material” includes materials containing cellulose and/or hemicellulose. Generally, these materials also contain xylan, lignin, protein, and carbohydrates, such as starch and sugar. Lignocellulose is generally found, for example, in the stems, leaves, hulls, husks, and cobs of plants or leaves, branches, and wood of trees. The process of converting a complex carbohydrate (such as starch or cellulose) into fermentable sugars is also referred to herein as “saccharification.” Fermentable sugars, as used herein, refers to simple sugars, such as glucose, xylose, arabinose, galactose, mannose, rhamnose, sucrose and fructose.

Biomass can include virgin biomass and/or non-virgin biomass such as agricultural biomass, commercial organics, construction and demolition debris, municipal solid waste, waste paper and yard waste. Common forms of biomass include trees, shrubs and grasses, wheat, wheat straw, sugar cane bagasse, corn, corn husks, corn kernel including fiber from kernels, products and by-products from milling of grains such as corn, wheat and barley (including wet milling and dry milling) as well as municipal solid waste, waste paper and yard waste. The biomass can also be, but is not limited to, herbaceous material, agricultural residues, forestry residues, municipal solid wastes, waste paper, and pulp and paper mill residues. “Agricultural biomass” includes branches, bushes, canes, corn and corn husks, energy crops, forests, fruits, flowers, grains, grasses, herbaceous crops, leaves, bark, needles, logs, roots, saplings, short rotation woody crops, shrubs, switch grasses, trees, vegetables, fruit peels, vines, sugar beet pulp, wheat midlings, oat hulls, and hard and soft woods (not including woods with deleterious materials). In addition, agricultural biomass includes organic waste materials generated from agricultural processes including farming and forestry activities, specifically including forestry wood waste. Agricultural biomass may be any of the aforestated singularly or in any combination or mixture thereof.

Biomass high in starch, sugar, or protein such as corn, grains, fruits and vegetables are usually consumed as food. Conversely, biomass high in cellulose, hemicellulose and lignin are not readily digestible and are primarily utilized for wood and paper products, animal feed, fuel, or are typically disposed. Generally, the substrate is of high lignocellulose content, including distillers' dried grains corn stover, corn cobs, rice straw, hay, sugarcane bagasse, and other agricultural biomass, switchgrass, forestry wastes, poplar wood chips, pine wood chips, sawdust, yard waste, and the like, including any combination of substrate.

In one embodiment, the lignocellulosic material is distillers' dried grains (DDG). DDG (also known as dried distiller's grain, or distiller's spent grain) is spent, dried grains recovered after alcohol fermentation. The lignocellulosic material can also be distiller's dried grain with soluble material recycled back (DDGS). While reference will be made herein to DDG for convenience and simplicity, it should be understood that both DDG and DDGS are contemplated as desired lignocellulosic materials. These are largely considered to be waste products and can be obtained after the fermentation of the starch derived from any of a number of grains, including corn, wheat, barley, oats, rice and rye. In one embodiment the DDG is derived from corn.

It should be noted that the distiller's grains do not necessarily have to be dried. Although the grains normally, currently dried, water and enzymes are added to the DDG substrate in the present invention. If the saccharification were done on site, the drying step could be eliminated and enzymes could be added to the distiller's grains without drying.

Due in part to the many components that comprise biomass and lignocellulosic materials, enzymes or a mixture of enzymes capable of degrading xylan, lignin, protein, and carbohydrates are needed to achieve saccharification. The present invention includes enzymes or compositions thereof with, for example, cellobiohydrolase, endoglucanase, xylanase, β-glucosidase, hemicellulase and chitinase activities.

The enzymes of the present invention may also be used for stone washing cellulosic fabrics such as cotton (e.g., denim), linen, hemp, ramie, cupro, lyocell, newcell, rayon and the like. See, for example, U.S. Pat. No. 6,015,707. The enzymes and compositions of the present invention are suitable for industrial textile applications in addition to the stone washing process. For example, cellulases are used in detergent compositions, either for the purpose of enhancing the cleaning ability of the composition or as a softening agent. When so used, the cellulase will degrade a portion of the cellulosic material, e.g., cotton fabric, in the wash, which facilitates the cleaning and/or softening of the fabric. The endoglucanase components of fungal cellulases have also been used for the purposes of enhancing the cleaning ability of detergent compositions, for use as a softening agent, and for use in improving the feel of cotton fabrics, and the like. Enzymes and compositions of the present invention may also be used in the treatment of paper pulp (e.g., for improving the drainage or for de-inking of recycled paper) or for the treatment of wastewater streams (e.g., to hydrolyze waste material containing cellulose, hemicellulose and pectins to soluble lower molecular weight polymers).

In one aspect, the present invention includes proteins isolated from, or derived from the knowledge of enzymes from, a fungus such as C. lucknowense or a mutant or other derivative thereof, and more particularly, from the fungal strain denoted herein as C1 (Accession No. VKM F-3500-D). Preferably, the proteins of the invention possess enzymatic activity. As described in U.S. Pat. No. 6,015,707 or U.S. Pat. No. 6,573,086, each of which is incorporated herein by reference for all purposes, a strain called C1 (Accession No. VKM F-3500-D), was isolated from samples of forest alkaline soil from Sola Lake, Far East of the Russian Federation. This strain was deposited at the All-Russian Collection of Microorganisms of Russian Academy of Sciences (VKM), Bakhurhina St. 8, Moscow, Russia, 113184, under the terms of the Budapest Treaty on the International Regulation of the Deposit of Microorganisms for the Purposes of Patent Procedure on Aug. 29, 1996, as Chrysosporium lucknowense Garg 27K, VKM-F 3500 D. Various mutant strains of C. lucknowense C1 have been produced and these strains have also been deposited at the All-Russian Collection of Microorganisms of Russian Academy of Sciences (VKM), Bakhurhina St. 8, Moscow, Russia, 113184, under the terms of the Budapest Treaty on the International Regulation of the Deposit of Microorganisms for the Purposes of Patent Procedure on Sep. 2, 1998. For example, Strain C1 was mutagenised by subjecting it to ultraviolet light to generate strain UV13-6 (Accession No. VKM F-3632 D). This strain was subsequently further mutated with N-methyl-N′-nitro-N-nitrosoguanidine to generate strain NG7C-19 (Accession No. VKM F-3633 D). This latter strain in turn was subjected to mutation by ultraviolet light, resulting in strain UV18-25 (VKM F-3631 D). Strain C1 was classified as a Chrysosporium lucknowense based on morphological and growth characteristics of the microorganism, as discussed in detail in U.S. Pat. No. 6,015,707 and U.S. Pat. No. 6,573,086.

In certain embodiments of the present invention, a protein of the invention comprises, consists essentially of, or consists of an amino acid sequence selected from: SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11, SEQ ID NO:14, SEQ ID NO:17, SEQ ID NO:20, SEQ ID NO:23, SEQ ID NO:26, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38, SEQ ID NO:41, SEQ ID NO:44, SEQ ID NO:47, SEQ ID NO:50, SEQ NO:53, SEQ ID NO:56, SEQ ID NO:59, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77, SEQ ID NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, SEQ ID NO:92, or SEQ ID NO:94. The present invention also includes homologues of any of the above sequences, including fragments and sequences having a given identity to any of the above sequences, wherein the homologue or fragment has at least one biological activity of the wild-type protein, as described herein.

In general, the proteins disclosed herein possess carbohydrase enzymatic activity, or the ability to degrade carbohydrate-containing materials. More specifically, the proteins may possess cellulase activity such as endoglucanase activity (e.g., 1,4-β-D-glucan-4-glucanohydrolases), exoglucanase activity (e.g., 1,4-β-D-glucan cellobiohydrolases), and β-glucosidase activity. The proteins may possess hemicellulase activity such as endoxylanase activity, exoxylanase activity, or β-xylosidase activity. The proteins may possess laminarinase, xyloglucanase; galactanase, glucoamylase, pectate lyase, chitinase, exo-β-D-glucosaminidase, cellobiose dehydrogenase, acetylxylan esterase, ligninase, amylase, glucuronidase, ferulic acid esterase, arabinofuranosidase, pectin methyl esterase, arabinase, lipase, glucosidase or glucomannanase activities. Physical properties, biochemical characteristics and substrate specificities of proteins of the present invention are illustrated below.

As used herein, “carbohydrase” refers to any protein that catalyzes the hydrolysis of carbohydrates, “Glycoside hydrolase” or “glycosidase” refers to a protein that catalyzes the hydrolysis of the glycosidic bonds between carbohydrates or between a carbohydrate and a non-carbohydrate residue. Endoglucanases, cellobiohydrolases, β-glucosidases, α-glucosidases, xylanases, β-xylosidases, galactanases, α-galactosidases, β-galactosidases, α-amylases, glucoamylases, endo-arabinases, arabinofuranosidases, mannanases, β-mannosidases, pectinases, acetyl xylan esterases, acetyl mannan esterases, ferulic acid esterases, coumaric acid esterases, pectin methyl esterases, and chitinases are examples of glycosidases.

“Celluose” refers to a protein that catalyzes the hydrolysis of 1,4-β-D-glycosidic linkages in cellulose (such as bacterial cellulose, cotton, filter paper, phosphoric acid swollen cellulose, Avicel); cellulose derivatives (such as carboxymethylcellulose and hydroxyethylcellulose); plant lignocellulosic materials, beta-D-glucans or xyloglucans. Cellulose is a linear beta-(1-4) glucan consisting of anhydrocellobiose units. Endoglucanases, cellobiohydrolases, and β-glucosidases are examples of cellulases. “Endoglucanase” refers to a protein that catalyzes the hydrolysis of cellulose to oligosaccharide chains at random locations by means of an endoglucanase activity. “Cellobiohydrolase” refers to a protein that catalyzes the hydrolysis of cellulose to cellobiose via an exoglucanase activity, sequentially releasing molecules of cellobiose from the reducing or non-reducing ends of cellulose or cellooligosaccharides. “β-glucosidase” refers to an enzyme that catalyzes the conversion of cellobiose and oligosaccharides to glucose.

“Hemicellulase” refers to a protein that catalyzes the hydrolysis of hemicellulose, such as that found in lignocellulosic materials. Hemicellulose is a complex polymer, and its composition often varies widely from organism to organism, and from one tissue type to another. Hemicelluloses include a variety of compounds, such as xylans, arabinoxylans, xyloglucans, mannans, glucomannans, and galactomannans. Hemicellulose can also contain glucan, which is a general teem for beta-linked glucose residues. In general, a main component of hemicellulose is beta-1,4-linked xylose, a five carbon sugar. However, this xylose is often branched as beta-1,3 linkages or beta-1,2 linkages, and can be substituted with linkages to arabinose, galactose, mannose, glucuronic acid, or by esterification to acetic acid. The composition, nature of substitution, and degree of branching of hemicellulose is very different in dicotyledonous plants (dicots, i.e., plant whose seeds have two cotyledons or seed leaves such as lima beans, peanuts, almonds, peas, kidney beans) as compared to monocotyledonous plants (monocots; i.e., plants having a single cotyledon or seed leaf such as corn, wheat, rice, grasses, barley). In dicots, hemicellulose is comprised mainly of xyloglucans that are 1,4-beta-linked glucose chains with 1,6-alpha-linked xylosyl side chains. In monocots, including most grain crops, the principal components of hemicellulose are heteroxylans. These are primarily comprised of 1,4-beta-linked xylose backbone polymers with 1,2- or 1,3-beta linkages to arabinose, galactose and mannose as well as xylose modified by ester-linked acetic acids. Also present are branched beta glucans comprised of 1,3- and 1,4-beta-linked glucosyl chains. In monocots, cellulose, heteroxylans and beta glucans are present in roughly equal amounts, each comprising about 15-25% of the dry matter of cell walls. Hemicellulolytic enzymes, i.e. hemicellulases, include both endo-acting and exo-acting enzymes, such as xylanases. β-xylosidases, galactanases, α-galactosidases, β-galactosidases, endo-arabinases, arabinofuranosidases, mannanases, β-mannosidases. Hemicellulases also include the accessory enzymes, such as acetylesterases, ferulic acid esterases, and coumaric acid esterases. Among these, xylanases and acetyl xylan esterases cleave the xylan and acetyl side chains of xylan and the remaining xylo-oligomers are unsubstituted and can thus be hydrolysed with β-xylosidase only. In addition, several less known side activities have been found in enzyme preparations which hydrolyze hemicellulose. Accordingly, xylanases, acetylesterases and β-xylosidases are examples of hemicellulases.

“Xylanase” specifically refers to an enzyme that hydrolyzes the β-1,4 bond in the xylan backbone, producing short xylooligosaccharides.

β-Mannanases hydrolyze mannan-based hemicelluloses (mannan, glucomannan, galactomannan) and produce short-1,4-mannooligosaccharides.

“Galactanase” or “arabinogalactan endo-1,4-β-galactosidase” refers to a protein that catalyzes the hydrolysis of endo-1,4-β-D-galactosidic linkages in arabinogalactans.

“Glucoamylase” refers to a protein that catalyzes the hydrolysis of terminal 1,4-linked α-D-glucose residues successively from non-reducing ends of the chains with the release of β-D-glucose.

“Chitinase” or “exo-β-D-chitinase” refers to a protein that catalyzes the hydrolysis of N-acetyl-β-D-glucosaminide, 1,4-β-linkages in chitin and chitodextrins.

“α-L-arabinofuranosidase” or “arabinofuranosidase” refers to a protein that hydrolyzes arabinofuranosyl-containing hemicelluloses. Some of these enzymes remove arabinofuranoside residues from O-2 and/or O-3 single substituted xylose residues, as well as from O-2 and O-3 doubly substituted xylose residues “Endo-arabinase” refers to a protein that catalyzes the hydrolysis of 1,5-α-arabinofuranosidic linkages in 1,5-arabinans.

“β-xylosidase” refers to a protein that hydrolyzes short 1,4-β-D-xylooligomers into xylose.

“Acetyl xylan esterase” refers to a protein that catalyzes the removal of the acetyl groups from xylose residues. “Acetyl mannan esterase” refers to a protein that catalyzes the removal of the acetyl groups from mannose residues. “Feruloyl esterase” or “ferulic acid esterase” refers to a protein that hydrolyzes the ester bond between the arabinose substituent group and ferulic acid. “Coumaric acid esterase” refers to a protein that hydrolyzes the ester bond between the arabinose substituent group and coumaric acid. Acetyl xylan esterases, ferulic acid esterases and pectin methyl esterases are examples of carbohydrate esterases.

“Pectate lyase” refers to a protein that catalyzes the cleavage of 1,4-α-D-galacturonan in oligosaccharide substrates.

Glycosidases (glycoside hydrolases; GH), a large family of enzymes that includes cellulases and hemicellulases, catalyze the hydrolysis of glycosidic linkages, predominantly in carbohydrates. Glycosidases such as the proteins of the present invention may be assigned to families on the basis of sequence similarities, and there are now over 100 different such families defined (see the CAZy (Carbohydrate Active EnZymes database) website, maintained by the Architecture of Fonction de Macromolecules Biologiques of the Centre National de la Recherche Scientifique, which describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds; Coutinho, P. M. & Henrissat, B. (1999) Carbohydrate-active enzymes: an integrated database approach. In “Recent Advances in Carbohydrate Bioengineering”, H. J. Gilbert, G. Davies, B. Henrissat and B. Svensson eds., The Royal Society of Chemistry, Cambridge, pp. 3-12). Because there is a direct relationship between the amino acid sequence of a protein and its folding similarities, such a classification reflects the structural features of these enzymes and their substrate specificity. Such a classification system can help to reveal the evolutionary relationships between these enzymes and provide a convenient tool to determine information such as a enzyme's activity and function. Thus, enzymes assigned to a particular family based on sequence homology with other members of the family are expected to have similar enzymatic activities and related substrate specifities. CAZy family classifications also exist for glycosyltransferases (GT), polysaccharide lyases (PL), and carbohydrate esterases (CE). Likewise, sequence homology may be used to identify particular domains within proteins, such as cellulose binding modules (CBMs; also known as cellulose binding domains (CBDs)). The CAZy homologies of proteins of the present invention are disclosed below.

Proteins of the present invention may also include homologues and fragments of the proteins disclosed herein. The protein fragments include, but are not limited to, fragments comprising a catalytic domain (CD) and/or a cellulose-binding domain (also known as a cellulose binding module (CBM); both are referred to herein as CBD). The identity and location of domains within proteins of the present invention are disclosed in detail below. The present invention encompasses all combinations of the disclosed domains. For example, a protein fragment may comprise a CD of a protein but not a CBD of the protein or a CBD of a protein but not a CD. Similarly, domains from different proteins may be combined. Protein fragments comprising a CD, CBD or combinations thereof for each protein disclosed herein can be readily produced using, standard techniques known in the art. In some embodiments, a protein fragment comprises a domain of a protein that has at least one biological activity of the full-length protein. Homologues of proteins of the invention that have at least one biological activity of the full-length protein are described in detail below. As used herein, the phrase “biological activity” of a protein refers to any function(s) exhibited or performed by the protein that is ascribed to the naturally occurring form of the protein as measured or observed in vitro or in vivo. In certain embodiments, a protein fragment comprises a domain of a protein that has the catalytic activity of the full-length enzyme. Specific biological activities of the proteins of the invention, and structures within the proteins that are responsible for the activities, are described below.

Cellobiohydrolases

Certain proteins of the present invention possess cellobiohydrolase enzymatic activity. For example, the polypeptides denoted herein as CBH Ia (SEQ ID NO:2), CBH Ib (SEQ ID NO:5), CBH IIa (SEQ ID NO:8), and CBH IIb (SEQ ID NO:11) possess cellobiohydrolase activity. These enzymes participate in the hydrolytic conversion of insoluble cellulose to cellooligosaccharides, with cellobiose being a primary product of the enzymatic catalysis.

The enzyme denoted CBH Ia is encoded by the genomic nucleic acid sequence represented herein as SEQ ID NO:1 and the cDNA sequence represented herein as SEQ ID NO:3. The CBH Ia nucleic acid sequence encodes a 526 amino acid sequence, represented herein as SEQ ID NO:2. The signal peptide for CBH Ia is located from positions 1 to about position 17 of SEQ ID NO:2, with the mature protein spanning from about position 18 to position 526 of SEQ NO:2. Within CBH Ia are two domains: a catalytic domain (CD) and a cellulose-binding domain (CBD). The amino acid sequence containing the CD of CBH Ia spans from a starting point of about position 19 of SEQ ID NO:2 to an ending point of about position 453 of SEQ ID NO:2. The amino acid sequence containing the CBD of CBH Ia spans from a starting point of about position 490 of SEQ ID NO:2 to an ending point of about position 519 of SEQ ID NO:2. Based on homology, CBH Ia can be assigned to CAZy Families GH 7 and COM 1. As evidenced below. CBH is exhibits cellobiohydrolase activity.

The enzyme denoted. CBH Ib is encoded by the nucleic acid sequence represented herein as SEQ ID NO:4 and the cDNA sequence represented herein as SEQ ID NO:6. The CBH Ib nucleic acid sequence encodes a 450 amino acid sequence, represented herein as SEQ ID NO:5. The signal peptide for CBH Ia is located from positions 1 to about position 20 of SEQ ID NO:5, with the mature protein spanning from about position 21 to position 450 of SEQ ID NO:5. Within CBH Ia is a catalytic domain (CD). The amino acid sequence containing the CD of CBH Ib spans from a starting point of about position 22 of SEQ ID NO:5 to an ending point of about position 450 of SEQ ID NO:5. Based on homology, CBH Ib can be assigned to CAZy Family GH 7. As evidenced below, CBH Ib exhibits cellobiohydrolase activity.

The enzyme denoted CBH IIa is encoded by the nucleic acid sequence represented herein as SEQ ID NO:7 and the cDNA sequence represented herein as SEQ ID NO:9. The CBH IIa nucleic acid sequences encodes a 395 amino acid sequence, represented herein as SEQ ID NO:8. The signal peptide for CBH IIa is located from positions 1 to about position 17 of SEQ ID NO:8, with the mature protein spanning from about position 18 to position 395 of SEQ ID NO:8. Within CBH IIa is a catalytic domain (CD). The amino acid sequence containing the CD of CBH IIa spans from a starting point of about position 40 of SEQ ID NO:8 to an ending point of about position 395 of SEQ ID NO:8. Based on homology, CBH IIa can be assigned to CAZy Family GH 6. As evidenced below, CBH IIa exhibits cellobiohydrolase activity.

The enzyme denoted CBH IIb is encoded by the nucleic acid sequence represented herein as SEQ ID NO:10 and the cDNA sequence represented herein as SEQ ID NO:12. The CBH IIb nucleic acid sequence encodes a 482 amino acid sequence, represented herein as SEQ ID NO:11. The signal peptide for CBH IIb is located from positions 1 to about position 17 of SEQ ID NO:11, with the mature protein spanning from about position 18 to position 482 of SEQ ID NO:11. Within CBH IIb are two domains: a catalytic domain (CD) and a cellulose-binding domain (CBD). The amino acid sequence containing the CBD of CBH IIb spans from a starting point of about position 27 of SEQ ID NO:11 to an ending point of about position 62 of SEQ ID NO:11. The amino acid sequence containing the CD of CBH IIb spans from a starting point of about position 125 of SEQ ID NO:11 to an ending point of about position 482 of SEQ ID NO:11. Based on homology, CBH IIb can be assigned to CAZy Families GH 6 and CBM 1. As evidenced below, CBH IIb exhibits cellobiohydrolase activity.

Physical properties, biochemical characteristics and substrate specificities of cellobiohydrolases of the present invention are illustrated in Tables 1 and 2 below. Physical and biochemical characteristics include molecular weight, isoelectric point, pH and temperature optima of enzymatic activity, and the stability of the enzymes after heating to 50° C. for five hours at pH 5.0 or 7.0. Substrate specificities demonstrating enzyme activity for the indicated substrates were determined using standard assays known in the art, such as those disclosed in the Examples below. FIG. 1 illustrates the specific activity of cellobiohydrolases of the present invention toward substrates selected from Table 2.

TABLE 1 Physical and Biochemical Properties of C1 Cellobiohydrolases Stability Stability Enzyme SEQ ID NO MW (kDa) pI pH (50%) T ° C. (50%) pH 5.0 pH 7.0 CBH Ia 2 65 4.5 5.0 60 99% 96% (3.5-6.5) (45−>80) CBH Ia 2 (CD 52 4.5 5.0 60 97% 95% (CD) Only) (3.5-6.5) (45−>80) CBH Ib 5 60 3.8 4.7 65 80% 80% (3.3-6.3) (50−>80) CBH IIa 8 43 4.2 5.0 60 98% 70% (3.5-6.5) (50-72)  CBH IIb 11  70 5.6 5.0 60 100%  80% (<3.0-6.5)  (50-75)  MW = Molecular Weight, kiloDaltons (kDa) pI = isoelectric point pH (50%) = pH optimum of enzyme activity (range of at least 50% activity) T ° C. (50%) = Temperature optimum of enzyme activity (range of at least 50% activity) Stability pH 5.0 = residual enzyme activity after 5 hour incubation at 50° C., pH 5.0 Stability pH 7.0 = residual enzyme activity after 5 hour incubation at 50° C., pH 7.0

TABLE 2 Substrate Specificities of C1 Cellobiohydrolases (Activity Towards Specific Substrates (units/mg)) CBH Ia Substrate CBH Ia (CD) CBH Ib CBH IIa CBH IIb CMC 0.2 0.2 0.3 1.1 0.1 (S—N Assay) CMC 0.01 0.02 0.02 0.6 0.01 (Viscometric) β-glucan <0.1 <0.1 <0.1 2.0 0.2 Avicel 0.21 0.10 0.12 0.08 0.22 Birchwood Xylan 0 0 0 1.4 0.03 Xyloglucan 0 0 0 0 0 Laminarin 0 0 0 0 0 Arabinan 0 0 0 0.1 0 Galactan 0 0 0 0 0 Galactomannan 0 0 0 0 0 p-NPh-β-D- 0.021 0.025 0.02 0 0 cellobioside p-NPh-β-D- 0.12 0.11 0.09 0 0 lactoside

pH and temperature dependencies of cellobiohydrolases of the present invention are illustrated in Tables 3 and 4 below. pH and temperature dependencies were determined using the Avicel cellulase assay described in Example 5 below. pH dependencies were assayed by varying the pH at 40° C. for one hour, while temperature dependencies were assayed by varying the temperature at pH 5.0 for one hour. The temperature/pH that exhibited the highest enzyme activity was set at 100% in the tables below, with the remaining values expressed a percentage of this standard. The pH and temperature dependencies of the cellobiohydrolases are also illustrated graphically in FIGS. 2 and 3, respectively.

TABLE 3 pH Dependency of C1 Cellobiohydrolases (% Activity) CBH Ia pH CBH Ia (CD) CBH Ib CBH IIa CBH IIb 3 23 35 22 21 72 3.55 50 50 48 50.0 87 3.9 58 61 85 68 89 4.3 75 80 95 85 91 4.7 95 95 100 99 95 5.08 100 100 92 100 100 5.6 98 98 75 98 98 6 77 78 58 78 94 6.6 48 49 46 51.6 50 7.1 17.4 20 20 42 30 7.5 2 8 23 10

TABLE 4 Temperature Dependency of C1 Cellobiohydrolases (% Activity) CBH Ia Temp ° C. CBH Ia (CD) CBH Ib CBH IIa CBH IIb 30 11.0 10 35 20 20 20.0 18 40 39 32 28 30 45 50 48 43 41 50 62 55 25 55 55.6 55 82 67 54 78 73 60 95 82 92 100 89 65 100 100 100 90 100 70 85 92 29 64 76 75 40 75 6 40 36.5 80 15 20 2 20 23

Endoglucanases

Some proteins of the present invention possess endo-1,4-β-glucanase enzymatic activity. For example, the polypeptides EG I (SEQ ID NO:14), EG II (SEQ ID NO:94), EG III (SEQ ID NO:17), EG V (SEQ ID NO:20), and EG VI (SEQ ID NO:23) possess endo-1,4-β-glucanase activity. As with the cellobiohydrolases described above, these endoglucanases also participate in the hydrolytic conversion of insoluble cellulose to cellooligosaccharides, with cellobiose being a primary product of the enzymatic catalysis.

The enzyme denoted EG I is encoded by the nucleic acid sequence represented herein as SEQ ID NO:13 and the cDNA sequence represented herein as SEQ ID NO:15. The EG I nucleic acid sequence encodes a 456 amino acid sequence, represented herein as SEQ ID NO:14. The signal peptide for EG I is located from positions 1 to about position 20 of SEQ ID NO:14, with the mature protein spanning from about position 21 to position 456 of SEQ ID NO:14. Within EG I is a catalytic domain (CD). The amino acid sequence containing the CD of EG I spans from a starting point of about position 22 of SEQ ID NO:14 to an ending point of about position 420 of SEQ ID NO:14. Based on homology, EG I can be assigned to CAZy Family GH 7. As evidenced below, EG I exhibits endoglucanase activity.

The enzyme denoted EG ii is a 389 amino acid sequence, represented herein as SEQ ID NO:94. The signal peptide for EG II is located from positions 1 to about position 16 of SEQ ID NO:94, with the mature protein spanning from about position 17 to position 389 of SEQ ID NO:94. Within EG II are two domains: a catalytic domain (CD) and a cellulose-binding domain (CBD). The amino acid sequence containing the CBD of EG II spans from a starting point of about position 17 of SEQ ID NO:94 to an ending point of about position 52 of SEQ ID NO:94. The amino acid sequence containing the CD of EG II spans from a starting point of about position 84 of SEQ ID NO:94 to an ending point of about position 388 of SEQ ID NO:94. As evidenced below, EG II exhibits endoglucanase activity.

The enzyme denoted EG III is encoded by the nucleic acid sequence represented herein as SEQ NO:16 and the cDNA sequence represented herein as SEQ ID NO:18. The EG III nucleic acid sequence encodes a 247 amino acid sequence, represented herein as SEQ ID NO:17. The signal peptide for EG III is located from positions 1 to about position 15 of SEQ ID NO:17, with the mature protein spanning from about position 16 to position 247 of SEQ ID NO:17. Within EG III is a catalytic domain (CD). The amino acid sequence containing the CD of EG III spans from a starting point of about position 91 of SEQ ID NO:17 to an ending point of about position 247 of SEQ ID NO:17. Based on homology, EG III can be assigned to CAZy Family GH 12. As evidenced below, EG III exhibits endoglucanase activity.

The enzyme denoted EG V is encoded by the nucleic acid sequence represented herein as SEQ ID NO:119 and the cDNA sequence represented herein as SEQ ID NO:21. The EG V nucleic acid sequence encodes a 225 amino acid sequence, represented herein as SEQ ID NO:20. The signal peptide for EG V is located from positions 1 to about position 18 of SEQ ID NO:20, with the mature protein spanning from about position 19 to position 225 of SEQ ID NO:20. Within EG V is a catalytic domain (CD). The amino acid sequence containing the CD of EG V spans from a starting point of about position 23 of SEQ ID NO:20 to an ending point of about position 224 of SEQ ID NO:20. Based on homology, EG V can be assigned to CAZy Family GH 45. As evidenced below, EG V exhibits endoglucanase activity.

The enzyme denoted EG VI is encoded by the nucleic acid sequence represented herein as SEQ ID NO:22 and the cDNA sequence represented herein as SEQ ID NO:24. The EG VI nucleic acid sequence encodes a 381 amino acid sequence, represented herein as SEQ ID NO:23. The signal peptide for EG VI is located from positions 1 to about position 18 of SEQ ID NO:23, with the mature protein spanning from about position 119 to position 38.1 of SEQ ID NO:23. Within EG VI is a catalytic domain (CD). The amino acid sequence containing the CD of EG VI spans from a starting point of about position 33 of SEQ ID NO:23 to an ending point of about position 378 of SEQ ID NO:23. Based on homology, EG VI can be assigned to CAZy Family GH 6. As evidenced below, EG VI exhibits endoglucanase activity.

Physical properties, biochemical characteristics and substrate specificities of endoglucanases of the present invention are illustrated in Tables 5 and 6 below. Physical and biochemical characteristics include molecular weight, isoelectric point, pH and temperature optima of enzymatic activity, and the stability of the enzymes after heating to 50° C. for five hours at pH 5.0 or 7.0. Substrate specificities demonstrating enzyme activity for the indicated substrates were determined using standard assays known in the art, such as those disclosed in the Examples below. FIG. 1 illustrates the specific activity of endoglucanases of the present invention toward substrates selected from Table 6.

TABLE 5 Physical and Biochemical Properties of C1 Endoglucanases Stability Stability Enzyme SEQ ID NO MW (kDa) pI pH (50%) T ° C. (50%) pH 5.0 pH 7.0 EG I 14 60 3.7 4.8 60 80% 80% (3.5-7.5) (43-76) EG II 97 51 4.8 4.7 70 93% 93% (3.5-7.5) (53-77) EG II 97 (CD 44 6.0 5.2 70 90% 90% (CD) Only) (3.5-7.5) (53-77) EG III 17 28 5.7 5.3 60 92% 74% (3.8-7.0) (30-75) EG V 20 25 4.0 5.5 65 95% 92% (3.5-8.5) (50-75) EG VI 23 47 5.7 6.0 70 60% 75%  (4.5−>8.5) (40-82) MW = Molecular Weight. kiloDaltons (kDa) pI = isoelectric point pH (50%) = pH optimum of enzyme activity (range of at least 50% activity) T ° C. (50%) = Temperature optimum of enzyme activity (range of at least 50% activity) Stability pH 5.0 = residual enzyme activity after 5 hour incubation at 50° C., pH 5.0 Stability pH 7.0 = residual enzyme activity after 5 hour incubation at 50° C., pH 7.0

TABLE 6 Substrate Specificities of C1 Endoglucanases (Activity Towards Specific Substrates (units/mg)) EG II Substrate EG I EG II (CD) EG III EG V EG VI CMC 12 52 59 11 17 14 (S—N Assay) CMC 5 46 39 19 20 6 (Viscometric) β-glucan 18 75 74 125 5.3 18 Avicel 0.08 0.19 0.06 0.02 0.06 0.07 Birchwood Xylan 0 0.18 0.07 0.2 0 0.08 Xyloglucan 0 0 0 15.6 1.9 0 Laminarin 0 0.1 0.1 0 0 0 Arabinan 0 0 0.3 0 0 0 Galactan 0 0 0.6 0 0 0.1 Galactomannan 0 1.1 1 0 0.1 0 p-NPh-β-D- 0.12 0 0 0 0 0 cellobioside p-NPh-β-D- 0.27 0 0 0 0 0 lactoside

pH and temperature dependencies of endoglucanases of the present invention are illustrated in Tables 7 and 8 below. pH and temperature dependencies were determined using the CMC cellulase assay described in Example 3 below. pH dependencies were assayed by varying the pH at 50° C. for five minutes, while temperature dependencies were assayed by varying the temperature at pH 5.0 for five minutes. The temperature/pH that exhibited the highest enzyme activity was set at 100% in the tables below, with the remaining values expressed a percentage of this standard. The pH and temperature dependencies of the endoglucanases are also illustrated graphically in FIGS. 4 and 5, respectively.

TABLE 7 pH Dependency of C1 Endoglucanases (% Activity) EG II pH EG I EG II (CD) EG III EG V EG VI 2.7 9 23 16 0 16.5 8 3.34 30 39 29 10 48 17 4.04 88 87 77 60 81 37 4.777 100 100 95 98 94.5 75 5.36 98 96 100 100 100 97 6.06 87 86 96 89 98 100 6.73 74 75 81 70 88 96 7.38 55 58 64 38 76.5 91 8 33 43 38 15 67 75 8.44 23 32 25 8 52 68

TABLE 8 Temperature Dependency of C1 Endoglucanases (% Activity) EG II Temp ° C. EG I EG II (CD) EG III EG V EG VI 30 22.5 19 10.5 55.2 22 24.7 35 30.5 20 12 69.1 26 37.0 40 42.3 24 20.7 80.6 37 52 45 61.1 27 25 86.3 45 68.5 50 83.3 35.4 32 93.2 51 79.8 55 95.5 55 56 97.5 70 89.0 60 100 72 71 100 83.3 96.1 65 93.5 90 92 95.9 100 99 70 77.6 100 100 87.9 88 100 75 57.3 62 70 57.5 60 82.2 80 32.4 31 35 13.4 33 57.5

Xylanases

Certain proteins of the present invention possess xylanase enzymatic activity. For example, the polypeptides Xyl 1 (SEQ ID NO:26), Xyl 2 (SEQ ID NO:29), Xyl 3 (SEQ ID NO:32), Xyl 4 (SEQ ID NO:35). Xyl 5 (SEQ ID NO:38), and Xyl 6 (SEQ ID NO:41) possess xylanase activity. These xylanases participate in the hydrolytic conversion of hemicellulose into xylose.

The enzyme denoted Xyl 1 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:25 and the cDNA sequence represented herein as SEQ ID NO:27. The Xyl 1 nucleic acid sequence encodes a 384 amino acid sequence, represented herein as SEQ ID NO:26. The signal peptide for Xyl 1 is located from positions 1 to about position 17 of SEQ ID NO:26, with the mature protein spanning from about position 18 to position 384 of SEQ ID NO:26. Within Xyl 1 are two domains: a catalytic domain (CD) and a cellulose-binding domain (CBD). The amino acid sequence containing the CBD of Xyl 1 spans from a starting point of about position 18 of SEQ ID NO:26 to an ending point of about position 53 of SEQ ID NO:26. The amino acid sequence containing the CD of Xyl 1 spans from a starting point of about position 83 of SEQ ID NO:26 to an ending point of about position 384 of SEQ ID NO:26. Based on homology, Xyl 1 can be assigned to CAZy Families GH 10 and CBM 1. As evidenced below, Xyl 1 exhibits xylanase activity.

The enzyme denoted Xyl 2 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:28 and the cDNA sequence represented herein as SEQ ID NO:30. The Xyl 2 nucleic acid sequence encodes a 221 amino acid sequence, represented herein as SEQ ID NO:29. The signal peptide for Xyl 2 is located from positions 1 to about position 18 of SEQ ID NO:29, with the mature protein spanning from about position 19 to position 221 of SEQ ID NO:29. Within Xyl 2 is a catalytic domain (CD). The amino acid sequence containing the CD of Xyl 2 spans from a starting point of about position 25 of SEQ ID NO:29 to an ending point of about position 219 of SEQ ID NO:29. Based on homology. Xyl 2 can be assigned to CAZy Family GH 11. As evidenced below, Xyl 2 exhibits xylanase activity.

The enzyme denoted Xyl 3 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:31 and the cDNA sequence represented herein as SEQ ID NO:33. The Xyl 3 nucleic acid sequence encodes a 413 amino acid sequence, represented herein as SEQ NO:32. The signal peptide for Xyl 3 is located from positions 1 to about position 17 of SEQ ID NO:32, with the mature protein spanning from about position 18 to position 413 of SEQ ID NO:32. Within Xyl 3 are two domains: a catalytic domain (CD) and a cellulose-binding domain (CBD). The amino acid sequence containing the CD of Xyl 3 spans from a starting point of about position 18 of SEQ ID NO:32 to an ending point of about position 336 of SEQ ID NO:32. The amino acid sequence containing the CBD of Xyl 3 spans from a starting point of about position 377 of SEQ ID NO:32 to an ending point of about position 413 of SEQ ID NO:32. Based on homology. Xyl 3 can be assigned to CAZy Family GH 10. As evidenced below, Xyl 3 exhibits xylanase activity.

The enzyme denoted Xyl 4 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:34 and the cDNA sequence represented herein as SEQ ID NO:36. The Xyl 4 nucleic acid sequence encodes a 375 amino acid sequence, represented herein as SEQ ID NO:35. The signal peptide for Xyl 4 is located from positions 1 to about position 19 of SEQ ID NO:35, with the mature protein spanning from about position 20 to position 375 of SEQ ID NO:35. Within Xyl 4 is a catalytic domain (CD). The amino acid sequence containing the CD of Xyl 4 spans from a starting point of about position 31 of SEQ ID NO:35 to an ending point of about position 354 of SEQ ID NO:35. Based on homology, Xyl 4 can be assigned to CAZy Family GH 10. As evidenced below, Xyl 4 exhibits xylanase activity.

The enzyme denoted Xyl 5 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:37 and the cDNA sequence represented herein as SEQ ID NO:39. The Xyl 5 nucleic acid sequence encodes a 226 amino acid sequence, represented herein as SEQ ID NO:38. The signal peptide for Xyl 5 is located from positions 1 to about position 21 of SEQ ID NO:38, with the mature protein spanning from about position 22 to position 226 of SEQ ID NO:38. Within Xyl 5 is a catalytic domain (CD). The amino acid sequence containing the CD of Xyl 5 spans from a starting point of about position 42 of SEQ ID NO:38 to an ending point of about position 223 of SEQ ID NO:38. Based on homology, Xyl 5 can be assigned to CAZy Families GH 11 and CE 4. As evidenced below, Xyl 5 exhibits xylanase activity.

The enzyme denoted Xyl 6 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:40 and the cDNA sequence represented herein as SEQ ID NO:42. The Xyl 6 nucleic acid sequence encodes a 228 amino acid sequence, represented herein as SEQ ID NO:41. The signal peptide for Xyl 6 is located from positions 1 to about position 20 of SEQ ID NO:41, with the mature protein spanning from about position 21 to position 228 of SEQ ID NO:41. Within Xyl 6 is a catalytic domain (CD). The amino acid sequence containing the CD of Xyl 6 spans from a starting point of about position 37 of SEQ ID NO:41 to an ending point of about position 226 of SEQ ID NO:41. Based on homology, Xyl 6 can be assigned to CAZy Family GH 11. As evidenced below, Xyl 6 exhibits xylanase activity.

Physical properties, biochemical characteristics and substrate specificities of xylanases of the present invention are illustrated in Tables 9, 10, 11 and 12 below. Physical and biochemical characteristics include molecular weight, isoelectric point, pH and temperature optima of enzymatic activity, and the stability of the enzymes after heating to 50° C. for five hours at pH 5.0 or 7.0, or after heating to 80° C. for twenty seconds. Substrate specificities demonstrating enzyme activity for the indicated substrates (specific and non-specific) were determined using standard assays known in the art, such as those disclosed in the Examples below. The degree of xylan exhaustive hydrolysis of specific substrates is also indicated. FIG. 6 illustrates the specific activity of xylanases of the present invention toward substrates selected from Table 10.

TABLE 9 Physical and Biochemical Properties of C1 Xylanases Stability Stability Stability Enzyme SEQ ID NO MW (kDa) pI pH T ° C. pH 5.0 pH 7.0 80° C. Xyl 1 26 42 7.8 5.5-7.0 65-70 100% (81%) 100% (85%) 12% Xyl 1 26 (CD 31 8.9 5.5-7.0 65-70 100% (76%) 100% (88%) 19% (CD) Only) Xyl 2 29 24 7.9 5.7-7.5 70  84% (35%)  71% (25%) 23% Xyl 3 32 57 4.4 5.5-6.5 80-85 100% (90%) 100% (92%) 75% Xyl 3 32 (CD 46 4.3 5.5-6.5 80-85 100% (95%) 100% (97%) 98% (CD) Only) Xyl 4 35 38 4.8 5.0 80 100% (82%) 100% (70%) 82% Xyl 5 38 22 6.7 4.5 65  45% (35%) Unstable at 68% pH ≧ 7.0 Xyl 6 41 23 8.4 6.0 65-70  90% (12%)  95% (20%) 60% MW = Molecular Weight, kiloDaltons (kDa) pI = isoelectric point pH = pH optimum of enzyme activity T ° C. = Temperature optimum of enzyme activity Stability pH 5.0 = residual enzyme activity after 1 hour incubation at 50° C. (60° C.), pH 5.0 Stability pH 7.0 = residual enzyme activity after 1 hour incubation at 50° C. (60° C.), pH 7.0 Stability 80° C. = residual enzyme activity after 20 seconds at 80° C.

TABLE 10 Substrate Specificities of C1 Xylanases (Activity Towards Specific Substrates (units/mg)) Xyl 1 Xyl 3 Substrate Xyl 1 (CD) Xyl 2 Xyl 3 (CD) Xyl 4 Xyl 5 Xyl 6 Birchwood Xylan 65 83 395 39 85 32 300 169 Beechwood Xylan 66 71 329 47 88 36 300 188 Wheat Arabinoxylan 83 102 494 52 98 40 143 268 Wheat Arabinoxylan 83 82 198 52 78 24 57 107 (Insoluble) Arabinoxylan 96 100 485 63 107 42 320 329 from Oat Spelts Viscometric 1311 1382 2158 807 1210 234 2700 2452 Activity, Wheat Arabinoxylan

TABLE 11 Degree of Xylan Exhaustive Hydrolysis of Specific Substrates by C1 Xylanases (%) Xyl 1 Xyl 3 Substrate Xyl 1 (CD) Xyl 2 Xyl 3 (CD) Xyl 4 Xyl 5 Xyl 6 Birchwood Xylan 26 24 19 24 23 25 22 21 Beechwood Xylan 24 22 15 22 20 23 18 17 Wheat Arabinoxylan 26 28 15 30 29 24 18 17 Wheat Arabinoxylan 12 13 7 14 11 12 9 8 (Insoluble) Arabinoxylan 28 27 19 29 25 26 20 19 from Oat Spelts

TABLE 12 Substrate Specificities of C1 Xylanases (Activity Towards Non-Specific Substrates (units/mg)) Xyl 1 Xyl 3 Substrate Xyl 1 (CD) Xyl 2 Xyl 3 (CD) Xyl 4 Xyl 5 Xyl 6 CMC 0.65 1 0 0.12 0.2 0 0 0 Avicel 0 0 0 0 0 0 0 0 p-NPh-β-D- 0 0 0 0.3 0.6 0.3 0 0 xylopyranoside p-NPh-β-D- 0.36 0.42 0 0.84 1.6 4.0 0 0 cellobioside

pH and temperature dependencies of xylanases of the present invention are illustrated in Tables 13 and 14 below. pH and temperature dependencies were determined using the xylanase assay (on soluble xylan) described in Example 7 below. pH dependencies were assayed by varying the pH at 40° C. for 10 minutes, while temperature dependencies were assayed by varying the temperature at pH 5.0 for 10 minutes. The temperature/pH that exhibited the highest enzyme activity was set at 100% in the table below, with the remaining values expressed a percentage of this standard. The pH and temperature dependencies of the xylanases are also illustrated graphically in FIGS. 7 and 8, respectively.

TABLE 13 pH Dependency of C1 Xylanases (% Activity) Xyl 1 Xyl 3 pH Xyl 1 (CD) Xyl 3 (CD) pH Xyl 4 pH Xyl 2 pH Xyl 6 pH Xyl 5 2.5 0.00 0.46 1.83 0.42 3.0 0.37 3.1 0 2.35 0.00 2.44 0.00 3.53 22.00 25.48 39.99 25.32 3.5 36.33 3.8 5.89 3.53 14.25 3 13.65 4.67 70.23 73.56 74.68 71.26 4.0 78.51 4.2 26.66 4.42 45.85 3.5 36.97 4.92 85.63 83.69 84.23 86.62 4.5 94.89 4.8 70.06 4.92 75.55 4 80.39 5.57 100 97.00 97.22 95.00 5.0 100 5.3 90.00 5.57 94.76 4.5 100 6.03 99.59 100 98.33 97.53 5.5 89.22 5.8 97.26 6.03 100 5.1 70.32 6.64 97.33 95.34 100 100 6.0 73.65 6.4 100 6.64 96.92 5.5 45.14 7.1 95.46 90.08 90.43 91.99 6.5 52.16 6.9 99.05 7.1 78.61 5.81 29.11 7.61 90.76 85.16 79.49 79.90 7.0 40.83 7.9 89.62 7.61 60.77 6.75 0.00 8.71 72.12 62.86 61.10 63.44 8.0 19.64 9.5 4.40 8.71 21.99 7.2 0.00

TABLE 14 Temperature Dependency of C1 Xylanases (% Activity) Xyl 1 Xyl 3 Temp ° C. Xyl 1 (CD) Xyl 2 Xyl 3 (CD) Xyl 4 Xyl 5 Xyl 6 30 37.5 37.5 8.3 27.3 26.5 18.6 44.8 35.4 40 46.8 46.8 22.7 34.1 31.7 27.4 56.3 57.0 45 63.1 63.1 40.0 30.0 36.4 62.6 50 73.1 73.1 47.2 46.4 36.5 40.3 75.9 76.1 55 82.9 82.9 59.5 63.8 50.5 85.0 60 88.1 88.1 79.0 63.3 67.5 70.3 98.3 87.5 65 98.0 98.0 92.5 76.1 80.4 81.8 100.0 97.2 70 100.0 100.0 100.0 81.5 87.5 86.4 92.2 97.3 75 95.0 95.0 95.2 92.0 88.8 92.6 70.1 71.6 80 63.7 63.7 56.4 100.0 98.3 100.0 30.2 46.2 85 41.0 41.0 100.0 100.0 85.3 31.1 90 21.1 21.1 71.9 69.8 65.6 20.8

Additional Glycosidases

Certain proteins of the present invention possess glycosidase enzymatic activity, including β-glucosidase, galactanase, glucoamylase, endo-arabinase, and β-xylosidase activities. The polypeptides denoted herein as Bgl3A (SEQ ID NO:44), Gal53A (SEQ ID NO:47), Gla15A (SEQ ID NO:50), Abn1 (SEQ ID NO:89) and bxl2 (SEQ ID NO:92) possess glycosidase activity, as indicated below.

The enzyme Bgl3A is encoded by the nucleic acid sequence represented herein as SEQ ID NO:43 and the cDNA sequence represented herein as SEQ ID NO:45. The Bgl2A nucleic acid sequence encodes a 871 amino acid sequence, represented herein as SEQ ID NO:44. The signal peptide for Bgl3A is located from positions 1 to about position 19 of SEQ ID NO:44, with the mature protein spanning from about position 20 to position 871 of SEQ ID NO:44. Within Bgl3A is a catalytic domain (CD). The amino acid sequence containing the CD of Bgl3A spans from a starting point of about position 87 of SEQ ID NO:44 to an ending point of about position 643 of SEQ ID NO:44. Based on homology, Bgl3A can be assigned to CAZy Family GH 3.

The enzyme Gal53A is encoded by the nucleic acid sequence represented herein as SEQ ID NO:46 and the cDNA sequence represented herein as SEQ ID NO:48. The Gal53A nucleic acid sequence encodes a 350 amino acid sequence, represented herein as SEQ ID NO:47. The signal peptide for Gal53A is located from positions 1 to about position 18 of SEQ ID NO:47, with the mature protein spanning from about position 19 to position 350 of SEQ ID NO:47. Within Gal53A is a catalytic domain (CD). The amino acid sequence containing the CD of Gal53A spans from a starting point of about position 19 of SEQ ID NO:47 to an ending point of about position 334 of SEQ ID NO:47. Based on homology, Gal53A can be assigned to CAZy Family GH 53. As evidenced below, Gal53A exhibits galactanase (arabinogalactan endo-1,4-β-galactosidase) activity.

The enzyme Gla15A is encoded by the nucleic acid sequence represented herein as SEQ ID NO:49 and the cDNA sequence represented herein as SEQ ID NO:51. The Gla15A nucleic acid sequence encodes a 628 amino acid sequence, represented herein as SEQ ID NO:50. The signal peptide for Gla15A is located from positions 1 to about position 20 of SEQ ID NO:50, with the mature protein spanning from about position 21 to position 628 of SEQ ID NO:50. Within Gla15A are two domains: a catalytic domain (CD) and a starch-binding domain (CBM 20). The amino acid sequence containing the CD of Gla15A spans from a starting point of about position 28 of SEQ ID NO:50 to an ending point of about position 461 of SEQ ID NO:50. The amino acid sequence containing the starch-binding domain of Gla15A spans from a starting point of about position 51.8 of SEQ ID NO:50 to an ending point of about position 628 of SEQ ID NO:50. Based on homology, Gla15A can be assigned to CAZy Families GH 15 and CBM 20. As evidenced below, Gla15A exhibits glucoamylase activity.

The enzyme Abn1 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:88 and the cDNA sequence represented herein as SEQ ID NO:90. The Abn1 nucleic acid sequence encodes a 321 amino acid sequence, represented herein as SEQ ID NO:89. The signal peptide for Abn1 is located from positions 1 to about position 20 of SEQ ID NO:89, with the mature protein spanning from about position 21 to position 321 of SEQ ID NO:89. Within Abn1 is a catalytic domain (CD). The amino acid sequence containing the CD of Abn1 spans from a starting point of about position 27 of SEQ ID NO:89 to an ending point of about position 321 of SEQ ID NO:89. Based on homology, Abn1 can be assigned to CAZy Family GH 43. As illustrated below in Example 23, Abn1 exhibits endo-arabinase activity as measured by the ability to hydrolyze AZCL-arabinan (debranched). Abn1 also possesses significant homology (about 61% from amino acids 13 to 321 of Abn1) with a endo-arabinase from Aspergillus niger (Genbank Accession No. AAA32682; see also Flipphi et al., Appl. Microbiol. Biotechnol. 40:318 (1993)). Based on this degree of homology, Abn1 is expected to exhibit similar endo-arabinase enzymatic activity.

The enzyme Bxl2 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:91 and the cDNA sequence represented herein as SEQ ID NO:93. The Bxl2 nucleic acid sequence encodes a 733 amino acid sequence, represented herein as SEQ ID. NO:92. The signal peptide for Bxl2 is located from positions 1 to about position 17 of SEQ ID NO:92, with the mature protein spanning from about position 18 to position 733 of SEQ ID NO:92. Within Bxl2 is a catalytic domain (CD). The amino acid sequence containing the CD of Bxl2 spans from a starting point of about position 26 of SEQ ID NO:92 to an ending point of about position 602 of SEQ ID NO:92. Based on homology, Bxl2 can be assigned to CAZy Family GH 3. As illustrated below in Example 24, Bxl2 exhibits β-xylosidase activity. Bxl2 also possesses significant homology (about 70% from amino acids 28 to 733 of Bxl2) with a β-glucosidase from Hypocrea jecorina (Genbank Accession No. 17.13235A; see also Barnett et al., Biotechnol. 9:562 (1991)). Based on this degree of homology, Bxl2 is also expected to exhibit similar β-glucosidase enzymatic activity.

Pectate Lyases

Certain proteins of the present invention possess pectate lyase enzymatic activity. The polypeptide denoted herein as Pel1 (SEQ ID NO:53) possesses pectate lyase activity.

The enzyme Pel1 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:52 and the cDNA sequence represented herein as SEQ ID NO:54. The Pel1 nucleic acid sequence encodes a 375 amino acid sequence, represented herein as SEQ ID NO:53. The signal peptide for Pel1 is located from positions 1 to about position 20 of SEQ ID NO:53, with the mature protein spanning from about position 21 to position 375 of SEQ ID NO:53. Within Pel1 is a catalytic domain (CD). The amino acid sequence containing the CD of Pel1 spans from a starting point of about position 21 of SEQ ID NO:53 to an ending point of about position 375 of SEQ ID NO:53. As evidenced below, Pel1 exhibits pectate lyase activity.

Chitinases

Certain proteins of the present invention possess chitinase enzymatic activity. The polypeptides denoted herein as Chi18A (SEQ ID NO:56) and Gls2A (SEQ ID NO:59) possess chitinase activity.

The enzyme Chi18A is encoded by the nucleic acid sequence represented herein as SEQ ID NO:55 and the cDNA sequence represented herein as SEQ ID NO:57. The Chi18A nucleic acid sequence encodes a 426 amino acid sequence, represented herein as SEQ ID NO:56. The signal peptide for Chi18A is located from positions 1 to about position 23 of SEQ ID NO:56, with the mature protein spanning from about position 24 to position 426 of SEQ ID NO:56. Within Chi18A is a catalytic domain (CD). The amino acid sequence containing the CD of Chi18A spans from a starting point of about position 42 of SEQ ID NO:56 to an ending point of about position 386 of SEQ ID NO:56. Based on homology, Chi18A can be assigned to CAZy Family GH 18. As evidenced below, Chi18A exhibits chitinase activity.

The enzyme Gls2A is encoded by the nucleic acid sequence represented herein as SEQ ID NO:58 and the cDNA sequence represented herein as SEQ ID NO:60. The Gls2A nucleic acid sequence encodes a 907 amino acid sequence, represented herein as SEQ ID NO:59. The signal peptide for Gls2A is located from positions 1 to about position 20 of SEQ ID NO:59, with the mature protein spanning from about position 21 to position 907 of SEQ ID NO:59. Within Gls2A is a catalytic domain (CD). The amino acid sequence containing the CD of Gls2A spans from a starting point of about position 210 of SEQ ID NO:59 to an ending point of about position 764 of SEQ ID NO:59. Based on homology, Gls2A can be assigned to CAZy Family GH 2. As evidenced below, Gls2A exhibits chitinase (exo-β-D-chitinase) activity.

Carbohydrate Esterases

Certain proteins of the present invention possess carbohydrate esterase enzymatic activity, such as acetyl xylan esterase, ferulic acid esterase and pectin methyl esterase activity The polypeptides denoted herein as Axe3 (SEQ ID NO:62), FaeA1 (SEQ ID NO:65), FaeA2 (SEQ ID NO:68), FaeB2 (SEQ ID NO:71), Axe1 (SEQ ID NO:80). Axe2 (SEQ ID NO:83) and Pme1 (SEQ ID NO:86) possess carbohydrate esterase activity.

The enzyme Axe3 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:61 and the cDNA sequence represented herein as SEQ ID NO:63. The Axe3 nucleic acid sequence encodes a 313 amino acid sequence, represented herein as SEQ ID NO:62. The signal peptide for Axe3 is located from positions 1 to about position 21 of SEQ ID NO:62, with the mature protein spanning from about position 22 to position 313 of SEQ ID NO:62. Within Axe3 is a catalytic domain (CD). The amino acid sequence containing the CD of Axe3 spans from a starting point of about position 22 of SEQ ID NO:62 to an ending point of about position 255 of SEQ ID NO:62. Based on homology, Axe3 can be assigned to CAZy Family CE 1. As illustrated below in Example 19, Axe3 exhibits acetyl esterase enzymatic activity. Axe3 also possesses significant homology (about 69% from amino acids 41 to 312 of Axe3) with an acetyl xylan esterase from Penicillium purpurogenum (Genbank Accession No. AAM93261.1; see also Gordillo et al., Mycol. Res. 110:1129 (2006)). Based on this degree of homology. Axe3 is expected to exhibit similar acetyl xylan esterase enzymatic activity.

The enzyme FaeA1 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:64 and the cDNA sequence represented herein as SEQ ID NO:66. The FaeA1 nucleic acid sequence encodes a 279 amino acid sequence, represented herein as SEQ ID NO:65. The signal peptide for FaeA1 is located from positions 1 to about position 20 of SEQ ID NO:65, with the mature protein spanning from about position 21 to position 279 of SEQ ID NO:65. Within FaeA1 is a catalytic domain (CD). The amino acid sequence containing the CD of FaeA1 spans from a starting point of about position 33 of SEQ ID NO:65 to an ending point of about position 216 of SEQ TD NO:65. Based on homology, FaeA1 can be assigned to CAZy Family CE 1. As illustrated below in Example 20, FaeA1 exhibits ferulic acid esterase enzymatic activity. FaeA1 also possesses significant homology (about 51% from amino acids 22 to 264 of FaeA1) with a ferulic acid esterase from Aspergillus clavatus (Genbank Accession No. CAC85738). Based on this degree of homology, FaeA1 is expected to exhibit similar ferulic acid esterase enzymatic activity.

The enzyme FaeA2 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:67 and the cDNA sequence represented herein as SEQ ID NO:69. The FaeA2 nucleic acid sequence encodes a 302 amino acid sequence, represented herein as SEQ ID NO:68. The signal peptide for FaeA2 is located from positions 1 to about position 26 of SEQ ID NO:68, with the mature protein spanning from about position 27 to position 302 of SEQ ID NO:68. As illustrated below in Example 20, FaeA2 exhibits ferulic acid esterase enzymatic activity. FaeA2 also possesses significant homology (about 45% from amino acids 32 to 301 of FaeA2) with a ferulic acid esterase from Aspergillus clavatus (Genbank Accession No. CAC85738). Based on this degree of homology, FaeA2 is expected to exhibit similar ferulic acid esterase enzymatic activity.

The enzyme FaeB2 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:70 and the cDNA sequence represented herein as SEQ ID NO:72. The FaeB2 nucleic acid sequence encodes a 319 amino acid sequence, represented herein as SEQ ID NO:71. The signal peptide for FaeB2 is located from positions 1 to about position 22 of SEQ ID NO:71, with the mature protein spanning from about position 23 to position 31.9 of SEQ ID NO:71. Within FaeB2 is a catalytic domain (CD). The amino acid sequence containing the CD of FaeB2 spans from a starting point of about position 63 of SEQ ID NO:71 to an ending point of about position 278 of SEQ ID NO:71. As illustrated below in Example 20, FaeB2 exhibits ferulic acid esterase enzymatic activity. FaeB2 also possesses significant homology (about 68% from amino acids 46 to 319 of FaeB2) with a type B ferulic acid esterase from Neurospora crassa (Genbank Accession No. CAC05587). Based on this degree of homology, FaeB2 is expected to exhibit similar ferulic acid esterase enzymatic activity.

The enzyme Axe1 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:79 and the cDNA sequence represented herein as SEQ ID NO:81. The Axe1 nucleic acid sequence encodes a 303 amino acid sequence, represented herein as SEQ ID NO:80. The signal peptide for Axe1 is located from positions 1 to about position 21 of SEQ ID NO:80, with the mature protein spanning from about position 22 to position 303 of SEQ ID NO:80. Within Axe1 are two domains: a catalytic domain (CD) and a cellulose-binding domain (CBD). The amino acid sequence containing the CD of Axe1 spans from a starting point of about position 37 of SEQ ID NO:80 to an ending point of about position 246 of SEQ ID NO:80. The amino acid sequence containing the CBD of Axe1 spans from a starting point of about position 271 of SEQ ID NO:80 to an ending point of about position 303 of SEQ ID NO:80. Based on homology, Axe1 can be assigned to CAZy Families CE 5 and CBM 1. As illustrated below in Example 19, Axe1 exhibits acetyl esterase enzymatic activity. Axe1 also possesses significant homology (about 57% from amino acids 3 to 303 of Axe1) with a acetyl xylan esterase from Hypocrea jecorina (Genbank Accession No. CAA93247; see also Margolles-Clark et al., Eur. J. Biochem. 237:553 (1996)). Based on this degree of homology, Axe1 is expected to exhibit similar acetyl xylan esterase enzymatic activity.

The enzyme Axe2 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:82 and the cDNA sequence represented herein as SEQ ID NO:84. The Axe2 nucleic acid sequence encodes a 228 amino acid sequence, represented herein as SEQ ID NO:83. The signal peptide for Axe2 is located from positions 1 to about position 17 of SEQ ID NO:83, with the mature protein spanning from about position 18 to position 228 of SEQ ID NO:83. Within Axe2 is a catalytic domain (CD). The amino acid sequence containing the CD of Axe2 spans from a starting point of about position 26 of SEQ ID NO:83 to an ending point of about position 242 of SEQ ID NO:83. Based on homology, Axe2 can be assigned to CAZy Family CE 5. As illustrated below in Example 19, Axe2 exhibits acetyl esterase enzymatic activity. Axe2 also possesses significant homology (about 58% from amino acids 7 to 225 of Axe2) with a acetyl xylan esterase from Penicillium purpurogenum (Genbank Accession No. 059893; see also Egana et al., Biotechnol. Appl. Biochem. 24(1):33 (1996)). Based on this degree of homology, Axe2 is expected to exhibit similar acetyl xylan esterase enzymatic activity.

The enzyme Pme1 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:85 and the cDNA sequence represented herein as SEQ ID NO:87. The Pme1 nucleic acid sequence encodes a 331 amino acid sequence, represented herein as SEQ ID NO:86. The signal peptide for Pme1 is located from positions 1 to about position 27 of SEQ ID NO:86, with the mature protein spanning from about position 28 to position 331 of SEQ ID NO:86. Within Pme1 is a catalytic domain (CD). The amino acid sequence containing the CD of Pme1 spans from a starting point of about position 43 of SEQ ID NO:86 to an ending point of about position 327 of SEQ ID NO:86. Based on homology, Pme1 can be assigned to CAZy Family CE 8. As illustrated below in Example 22, Pme1 exhibits pectin methyl esterase enzymatic activity on substrates such as methylated pectin (e.g., the ability to hydrolyze citrus pectin with a degree of methylation of 65 leading to the formation of unsubstituted galacturonic acid). Pectin methyl esterases catalyze the hydrolysis of methylester groups of pectins such as those found in the cell wails of plants. Pme1 also possesses significant homology (about 55% from amino acids 7 to 331 of Pme1) with a pectin methyl esterase from Emericella nidulans (Genbank Accession No. ABF50865.1; see also Bauer et al. Proc. Natl. Acad. Sci. U.S.A. 103:11417 (2006)). Based on this degree of homology, Pme1 is expected to exhibit similar pectin methyl esterase enzymatic activity.

Arabinofuranosidases

Certain proteins of the present invention possess arabinofuranosidase enzymatic activity. The polypeptides denoted herein as Abf1 (SEQ ID NO:74) and Abf2 (SEQ ID NO:77) possess arabinofuranosidase activity.

The enzyme Abf1 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:73 and the cDNA sequence represented herein as SEQ ID NO:75. The Abf1 nucleic acid sequence encodes a 370 amino acid sequence, represented herein as SEQ ID NO:74. The signal peptide for Abf1 is located from positions 1 to about position 22 of SEQ ID NO:74, with the mature protein spanning from about position 23 to position 370 of SEQ ID NO:74. Within Abf1 are two domains: a catalytic domain (CD) and a cellulose-binding domain (CBD). The amino acid sequence containing the CD of Abf1 spans from a starting point of about position 24 of SEQ ID NO:74 to an ending point of about position 294 of SEQ ID NO:74. The amino acid sequence containing the CBD of Abf1 spans from a starting point of about position 339 of SEQ ID NO:74 to an ending point of about position 370 of SEQ ID NO:74. Based on homology. Abf1 can be assigned to CAZy Families CBM 1. CBM 13 and GH 62. As illustrated below in Example 21, Abf1 exhibits α-arabinofuranosidase enzymatic activity. Abf1 also possesses significant homology (about 70% from amino acids 19 to 322 of Abf1) with a arabinofuranosidase from Streptomyces thermoviolaceus (Genbank Accession No. JC7820; see also Tsujibo et al., Biosci. Biotechnol. Biochem. 66:434 (2002)). Based on this degree of homology, Abf1 is expected to exhibit similar arabinofuranosidase enzymatic activity.

The enzyme Abf2 is encoded by the nucleic acid sequence represented herein as SEQ ID NO:76 and the cDNA sequence represented herein as SEQ ID NO:78. The Abf2 nucleic acid sequence encodes a 321 amino acid sequence, represented herein as SEQ ID NO:77. The signal peptide for Abf2 is located from positions 1 to about position 19 of SEQ ID NO:77, with the mature protein spanning from about position 20 to position 321 of SEQ ID NO:77. Within Abf2 is a catalytic domain (CD). The amino acid sequence containing the CD of Abf2 spans from a starting point of about position 22 of SEQ ID NO:77 to an ending point of about position 291 of SEQ ID NO:77. Based on homology, Abf2 can be assigned to CAZy Family GH 62. As illustrated below in Example 21, Abf2 exhibits α-arabinofuranosidase enzymatic activity. Abf2 also possesses significant homology (about 75% from amino acids 21 to 315 of Abf2) with a arabinofuranosidase from Streptomyces thermoviolaceus (Genbank Accession No. JC7820; see also Tsujibo et al., Biosci. Biotechnol. Biochem. 66:434 (2002)). Based on this degree of homology, Abf2 is expected to exhibit similar arabinofuranosidase enzymatic activity.

Physical properties, biochemical characteristics and substrate specificities of the glycosidases, pectate lyases, chitinases, carbohydrate esterases, and arabinofuranosidases of the present invention are illustrated in Tables 15, 16, 17 and 18 below. Physical and biochemical characteristics include molecular weight, isoelectric point, pH and temperature optima of enzymatic activity, and the stability of the enzymes after heating to 50° C. for five hours at pH 5.0. Substrate specificities demonstrating enzyme activity for the indicated substrates (specific and non-specific) were determined using standard assays known in the art, such as those disclosed in the Examples below.

TABLE 15 Physical and Biochemical Properties of C1 Enzymes Stability Enzyme SEQ ID NO MW (kDa) pI pH (50%) T ° C. (50%) pH 5.0 Bgl3A 44 106  4.8 4.0 60  64% (2.5-7.0) (45-70) Gal53A 47 30 8.2 4.5 55-60 100% (2.7-6.0) (30-70) Gla15A 50 68 4.3 5.5 70  50% (3.5-7.0) Pel1 53 33 5.3 8.5 60-65  100%** (7.8-8.8) (30-70) Chi18A 56 43 4.0 7.5 70  76% (5.7-8.7 (60-75) Gls2A 59 80 6.6 5.9 70 100% (5.0-7.0) (55-75) Axe3 62 35 6.5-6.8 FaeA1 65 25-40 3.5-4.0 FaeA2 68   29.1* 4.87* FaeB2 71   29.3* 4.28* Abf1 74 35 7.3 and 8.5-9.0 Abf2 77 33 4.5-5.0 Axe1 80  28* 7.2* Axe2 83 27 6 Pme1 86   32.6* 8.79* Abn1 89   32.8* 5.57* bxl2 95   75.9* 4.8* MW = Molecular Weight, kiloDaltons (kDa) (*= Predicted) pI = isoelectric point (*= Predicted) pH (50%) = pH optimum of enzyme activity (range of at least 50% activity) T ° C. (50%) = Temperature optimum of enzyme activity (range of at least 50% activity) Stability pH 5.0 = residual enzyme activity after 3 hour incubation at 50° C., pH 5.0 **pH 8.5, 1 mM CaCl₂

TABLE 16 Substrate Specificities of C1 Enzymes (Activity Towards Substrates (units/mg)) Substrate Bgl3A Gal53A Pel1 CMC (S—N Assay) 1.5 0 0 β-glucan from Barley 18 0 0 Birchwood 0 0 0 GlucuronoXylan Wheat ArabinoXylan 0 0 0 Xyloglucan from 0 0 0 Tamarind Laminarin (β-1,3; β- 109 0 0 1,6) Polygalacturonic acid 0 0 70  (RS) Citrus Pectin 0 0 525*  (Viscosimetry, A235) Citrus Pectin 0 0 82* (Etherefication 89%, A235) Citrus Pectin 0 0 126*  (Etherefication 65%, A235) Citrus Pectin 0 0 133*  (Etherefication 26%, A235) Galactan 0 620 0 Arabinan 0 97 0 Debranched Arabinan Branched 0 90 0 Arabinogalactan 0 0 0 Galactomannan 0 0 0 p-NPh-β-D- 0.03 0 0 cellobioside p-NPh-β-D- 0 0 0 lactoside p-NPh-β-L- 0 0 0 arabinofuranoside p-NPh-β-L- 0 0 0 arabinopyranoside o-NPh-β-D- 0 0 0 xylopyranoside p-NPh-β-D- 39 0 0 glucopyranoside p-NPh-β-L- 0 0 0 galactopyranoside Cellobiose (β-1,4) 52 0 0 Laminaribiose (β-1,3) 86 0 0 α-Sophorose (β-1,2) 50 0 0 Gentibiose (β-1,6) 107 0 0 Maltose 0 0 0 *C1 pectate lyase is a Ca⁺²-dependent enzyme, so activities were measured in 1 mM of CaCl₂.

TABLE 17 Substrate Specificities of C1 Gla15A (Activity Towards Substrates (units/mg)) Substrate Glucoamylase Activity Starch soluble (potato) NS* 150 Amylose soluble (potato), NS 87 Amylopectin soluble (potato), NS 104 Pullulan (Aureobasidium pullulans) 11 Starch insoluble (potato) NS 35 Amylose insoluble (potato), NS 59 Amylopectin insoluble (potato), NS 43 Maltose** 18 Isomaltose** 1.2 Maltotriose** 48 Maltohexaose** 61 pNph-α-D-glucopiranoside 0

TABLE 18 Substrate Specificities of C1 Enzymes (Activity Towards Substrates (units/mg)) Substrate Chi18A Gls2A Chitosan soluble, 140 kDa 35 28 Chitin Colloid 8 0 CMC 0 0 β-glucan 0 0 Birchwood GlucuronoXylan 0 0 p-NPh-β-D-N-acetylglucosamine 0.1 0 Chitosan, 140 kDa viscometry 210 0

pH and temperature dependencies of certain enzymes of the present invention are illustrated in Tables 19 and 20 below. pH and temperature dependencies were determined using the standard assays with the substrate and conditions listed below:

Enzyme pH Temperature Bgl3A p-NPh-β-D-glucopyranoside Cellobiose Gla15A Potato Starch, 50° C., 10 minutes Potato Starch, pH 5.0, 10 minutes Chi18A Colloidal chitin, 50° C., 10 minutes Chitosan (140 kD), pH 5.0, 10 minutes Gls2A Chitosan (140 kD), 50° C., 10 minutes Chitosan (140 kD), pH 5.0, 10 minutes Gal53A¹ Arabinan branched, 50° C., 10 minutes Arabinan branched, pH 5.0, 10 minutes Gal53A² Galactan, 50° C., 10 minutes Not Applicable Pel1 A235, PGA + 1 mM CaCl₂ A235, PGA + 1 mM CaCl₂

The temperature/pH that exhibited the highest enzyme activity was set at 100% in the tables below, with the remaining values expressed a percentage of this standard. The pH and temperature dependencies of certain enzymes are also illustrated graphically in FIGS. 9 and 10, respectively.

TABLE 19 pH Dependency of C1 Enzymes (% Activity) pH Bgl3A Gla15A Chi18A Gls2a pH Gal53A¹ pH Gal53A² pH Pel1 2.0 2 2.6 50 37 2.45 39.5 2.9 0.3 3.0 70 43 2 0 2.73 55.6 3.51 26.5 3.53 90 51 2 3 3.5 70.4 4.22 93.9 7.25 2.8 4.0 100 78 2 10.3 4.05 89.3 4.62 97.4 7.75 41.9 4.57 98 90 8 40 4.5 100.0 4.90 97.7 8.05 70.5 5.0 93 97 20 50 4.95 75.6 5.45 100 8.18 88.8 5.5 83 100 30 64 5.5 70.6 6.02 95.8 8.42 100 6.0 72 96 57 100 6.02 48.2 6.51 91.6 8.88 49.6 6.5 58 83 62 65 6.47 34.5 7.03 71.9 8.99 33 7.0 47 50 83 37.8 7.03 19.8 7.50 51.7 9.5 5 7.5 30 25 100 7.5 17.8 8.00 42.2 8 17 1 98 9.04 17.1 9.11 1.7 9 25

TABLE 20 Temperature Dependency of C1 Enzymes (% Activity) Temp ° C. Bgl3A Gla15A Chi18A Gls2a Gal53A¹ Temp ° C. Pel1 25 10 21 6.9 30 10 20 15 46.6 30 15.2 35 18 21 18 40 36 20 25 22 80.3 39 29.6 45 48 19 36 32 47 51.5 50 65 20 40 43 92.1 55 95 44 42 53 56 82.5 60 100 62 47 60 100 61 100 65 80 88 60 80 97.1 67 94.8 70 48 100 100 100 59.8 72 33.9 75 15 5 53 53 80 12 15 85 90

As used herein, reference to an isolated protein or polypeptide in the present invention, including any of the enzymes disclosed herein, includes full-length proteins, fusion proteins, or any fragment or homologue of such a protein. More specifically, an isolated protein, such as an enzyme according to the present invention, is a protein (including a polypeptide or peptide) that has been removed from its natural milieu (i.e., that has been subject to human manipulation) and can include purified proteins, partially purified proteins, recombinantly produced proteins, synthetically produced proteins, proteins complexed with lipids, soluble proteins, and isolated proteins associated with other proteins, for example. As such, “isolated” does not reflect the extent to which the protein has been purified. Preferably, an isolated protein of the present invention is produced recombinantly. In addition, and by way of example, a “C. lucknowens protein” or “C. lucknowens enzyme” refers to a protein (generally including a homologue of a naturally occurring protein) from Chrysosporium lucknowense or to a protein that has been otherwise produced from the knowledge of the structure (e.g. sequence) and perhaps the function of a naturally occurring protein from Chrysosporium lucknowense. In other words, a C. lucknowens protein includes any protein that has substantially similar structure and function of a naturally occurring C. lucknowens protein or that is a biologically active (i.e., has biological activity) homologue of a naturally occurring protein from C. lucknowens as described in detail herein. As such, a C. lucknowens protein can include purified, partially purified, recombinant, mutated/modified and synthetic proteins. According to the present invention, the terms “modification” and “mutation” can be used interchangeably, particularly with regard to the modifications/mutations to the amino acid sequence of a C. lucknowens protein (or nucleic acid sequences) described herein. An isolated protein according to the present invention can be isolated from its natural source, produced recombinantly or produced synthetically.

According to the present invention, the terms “modification” and “mutation” can be used interchangeably, particularly with regard to the modifications/mutations to the primary amino acid sequences of a protein or peptide (or nucleic acid sequences) described herein. The term “modification” can also be used to describe post-translational modifications to a protein or peptide including, but not limited to, methylation, farnesylation, carboxymethylation, geranyl geranylation, glycosylation, phosphorylation, acetylation, myristoylation, prenylation, palmitation, and/or amidation. Modifications can also include, for example, complexing a protein or peptide with another compound. Such modifications can be considered to be mutations, for example, if the modification is different than the post-translational modification that occurs in the natural, wild-type protein or peptide.

As used herein, the term “homologue” is used to refer to a protein or peptide which differs from a naturally occurring protein or peptide (i.e., the “prototype” or “wild-type” protein) by minor modifications to the naturally occurring protein or peptide, but which maintains the basic protein and side chain structure of the naturally occurring form. Such changes include, but are not limited to: changes in one or a few amino acid side chains; changes one or a few amino acids, including deletions (e.g., a truncated version of the protein or peptide), insertions and/or substitutions; changes in stereochemistry of one or a few atoms; and/or minor derivatizations, including but not limited to: methylation, glycosylation, phosphorylation, acetylation, myristoylation, prenylation, palmitation, amidation and/or addition of glycosylphosphatidyl inositol. A homologue can have either enhanced, decreased, or substantially similar properties as compared to the naturally occurring protein or peptide. A homologue can include an agonist of a protein or an antagonist of a protein.

Homologues can be the result of natural allelic variation or natural mutation. A naturally occurring allelic variant of a nucleic acid encoding a protein is a gene that occurs at essentially the same locus (or loci) in the genome as the gene which encodes such protein, but which, due to natural variations caused by, for example, mutation or recombination, has a similar but not identical sequence. Allelic variants typically encode proteins having similar activity to that of the protein encoded by the gene to which they are being compared. One class of allelic variants can encode the same protein but have different nucleic acid sequences due to the degeneracy of the genetic code. Allelic variants can also comprise alterations in the 5′ or 3′ untranslated regions of the gene (e.g., in regulatory control regions). Allelic variants are well known to those skilled in the art.

Homologues can be produced using techniques known in the art for the production of proteins including, but not limited to, direct modifications to the isolated, naturally occurring protein, direct protein synthesis, or modifications to the nucleic acid sequence encoding the protein using, for example, classic or recombinant DNA techniques to effect random or targeted mutagenesis.

Modifications in protein homologues, as compared to the wild-type protein, either agonize, antagonize, or do not substantially change, the basic biological activity of the homologue as compared to the naturally occurring protein. Modifications of a protein, such as in a homologue, may result in proteins having the same biological activity as the naturally occurring protein, or in proteins having decreased or increased biological activity as compared to the naturally occurring protein. Modifications which result in a decrease in protein expression or a decrease in the activity of the protein, can be referred to as inactivation (complete or partial), down-regulation, or decreased action of a protein. Similarly, modifications Which result in an increase in protein expression or an increase in the activity of the protein, can be referred to as amplification, overproduction, activation, enhancement, up-regulation or increased action of a protein.

According to the present invention, an isolated protein, including a biologically active homologue or fragment thereof, has at least one characteristic of biological activity of a wild-type, or naturally occurring, protein. As discussed above, in general, the biological activity or biological action of a protein refers to any function(s) exhibited or performed by the protein that is ascribed to the naturally occurring form of the protein as measured or observed in vivo (i.e., in the natural physiological environment of the protein) or in vitro (i.e., under laboratory conditions). The biological activity of a protein of the present invention can include an enzyme activity (catalytic activity and/or substrate binding activity), such as cellulase activity, hemicellulase activity, β-glucanase activity, β-glucosidase activity, α-galactosidase activity, β-galactosidase activity, xylanase activity or any other activity disclosed herein. Specific biological activities of the proteins disclosed herein are described in detail above and in the Examples. Methods of detecting and measuring the biological activity of a protein of the invention include, but are not limited to, the assays described in the Examples section below. Such assays include, but are not limited to, measurement of enzyme activity (e.g., catalytic activity), measurement of substrate binding, and the like. It is noted that an isolated protein of the present invention (including homologues) is not required to have a biological activity such as catalytic activity. A protein can be a truncated, mutated or inactive protein, or lack at least one activity of the wild-type enzyme, for example. Inactive proteins may be useful in some screening assays, for example, or for other purposes such as antibody production.

Methods to measure protein expression levels of a protein according to the invention include, but are not limited to: western blotting, immunocytochemistry, flow cytometry or other immunologic-based assays; assays based on a property of the protein including but not limited to, ligand binding or interaction with other protein partners. Binding assays are also well known in the art. For example, a BIAcore machine can be used to determine the binding constant of a complex between two proteins. The dissociation constant for the complex can be determined by monitoring changes in the refractive index with respect to time as buffer is passed over the chip (O'Shannessy et al. Anal. Biochem. 212:457-468 (1993); Schuster et al., Nature 365:343-347 (1993)). Other suitable assays for measuring the binding of one protein to another include, for example, immunoassays such as enzyme linked immunoabsorbent assays (ELISA) and radioimmunoassays (RIA), or determination of binding by monitoring the change in the spectroscopic or optical properties of the proteins through fluorescence, UV absorption, circular dichrosim, or nuclear magnetic resonance (NMR).

Many of the enzymes and proteins of the present invention may be desirable targets for modification and use in the processes described herein. These proteins have been described in terms of function and amino acid sequence (and nucleic acid sequence encoding the same) of representative wild-type proteins. In one embodiment of the invention, homologues of a given protein (which can include related proteins from other organisms or modified forms of the given protein) are encompassed for use in the invention. Homologues of a protein encompassed by the present invention can comprise, consist essentially of, or consist of, in one embodiment, an amino acid sequence that is at least about 35% identical, and more preferably at least about 40% identical, and more preferably at least about 45% identical, and more preferably at least about 50% identical, and more preferably at least about 55% identical, and more preferably at least about 60% identical, and more preferably at least about 65% identical, and more preferably at least about 70% identical, and more preferably at least about 75% identical, and more preferably at least about 80% identical, and more preferably at least about 85% identical, and more preferably at least about 90% identical, and more preferably at least about 95% identical, and more preferably at least about 96% identical, and more preferably at least about 97% identical, and more preferably at least about 98% identical, and more preferably at least about 99% identical, or any percent identity between 35% and 99%, in whole integers (i.e., 36%, 37%, etc.), to an amino acid sequence disclosed herein that represents the amino acid sequence of an enzyme or protein according to the invention (including a biologically active domain of a full-length protein). Preferably, the amino acid sequence of the homologue has a biological activity of the wild-type or reference protein or of a biologically active domain thereof (e.g., a catalytic domain).

In one embodiment, a protein of the present invention comprises, consists essentially of, or consists of an amino acid sequence that is less than 100% identical to an amino acid sequence selected from: SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11, SEQ ID NO:14, SEQ ID NO:17, SEQ ID NO:20, SEQ ID NO:23, SEQ ID NO:26, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38, SEQ ID NO:41, SEQ ID NO:44, SEQ ID NO:47, SEQ ID NO:50, SEQ ID NO:53, SEQ ID NO:56, SEQ ID NO:59, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77, SEQ ID NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, SEQ ID NO:92, or SEQ ID NO:94 (i.e., a homologue). In another aspect of the invention, a homologue according to the present invention has an amino acid sequence that is less than about 99% identical to any of such amino acid sequences, and in another embodiment, is less than about 98% identical to any of such amino acid sequences, and in another embodiment, is less than about 97% identical to any of such amino acid sequences, and in another embodiment, is less than about 96% identical to any of such amino acid sequences, and in another embodiment, is less than about 95% identical to any of such amino acid sequences, and in another embodiment, is less than about 94% identical to any of such amino acid sequences, and in another embodiment, is less than about 93% identical to any of such amino acid sequences, and in another embodiment, is less than about 92% identical to any of such amino acid sequences, and in another embodiment, is less than about 91% identical to any of such amino acid sequences, and in another embodiment, is less than about 90% identical to any of such amino acid sequences, and so on, in increments of whole integers.

As used herein, unless otherwise specified, reference to a percent (%) identity refers to an evaluation of homology which is performed using: (1) a BLAST 2.0 Basic BLAST homology search using blastp for amino acid searches and blastn, for nucleic acid searches with standard default parameters, wherein the query sequence is filtered for low complexity regions by default (described in Altschul, S. F., Madden, T. L., Schääffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.” Nucleic Acids Res. 25:3389-3402, incorporated herein by reference in its entirety); (2) a BLAST 2 alignment (using the parameters described below); (3) PSI-BLAST with the standard default parameters (Position-Specific Iterated BLAST; and/or (4) CAZy homology determined using standard default parameters from the Carbohydrate Active EnZymes database (Coutinho, P. M. & Henrissat, B. (1999) Carbohydrate-active enzymes: an integrated database approach. In “Recent Advances in Carbohydrate Bioengineering”, H. J. Gilbert, G. Davies, B. Henrissat and B. Svensson eds., The Royal Society of Chemistry, Cambridge, pp. 3-12).

It is noted that due to some differences in the standard parameters between BLAST 2.0 Basic BLAST and BLAST 2, two specific sequences might be recognized as having significant homology using the BLAST 2 program, whereas a search performed in BLAST 2.0 Basic BLAST using one of the sequences as the query sequence may not identify the second sequence in the top matches. In addition, PSI-BLAST provides an automated, easy-to-use version of a “profile” search, which is a sensitive way to look for sequence homologues. The program first performs a gapped BLAST database search. The PSI-BLAST program uses the information from any significant alignments returned to construct a position-specific score matrix, which replaces the query sequence for the next round of database searching. Therefore, it is to be understood that percent identity can be determined by using anyone of these programs.

Two specific sequences can be aligned to one another using BLAST 2 sequence as described in Tatusova and Madden, (1999), “Blast 2 sequences—a new tool for comparing protein and nucleotide sequences”, FEMS Microbiol Lett. 174:247-250, incorporated herein by reference in its entirety. BLAST 2 sequence alignment is performed in blastp or blastn using the BLAST 2.0 algorithm to perform a Gapped BLAST search (BLAST 2.0) between the two sequences allowing for the introduction of gaps (deletions and insertions) in the resulting alignment. For purposes of clarity herein, a BLAST 2 sequence alignment is performed using the standard default parameters as follows.

For blastn, using 0 BLOSUM62 matrix:

-   -   Reward for match=1     -   Penalty for mismatch=−2     -   Open gap (5) and extension gap (2) penalties     -   gap x_dropoff (50) expect (10) word size (11) filter (on)         For blastp, using 0 BLOSUM62 matrix:     -   Open gap (11) and extension gap (1) penalties     -   gap x_dropoff (50) expect (10) word size (3) filter (on).

A protein of the present invention can also include proteins having an amino acid sequence comprising at least 10 contiguous amino acid residues of any of the sequences described herein (i.e., 10 contiguous amino acid residues having 100% identity with 10 contiguous amino acids of SEQ ID NO:2). In other embodiments, a homologue of a protein amino acid sequence includes amino acid sequences comprising at least 20, or at least 30, or at least 40, or at least 50, or at least 75, or at least 100, or at least 125, or at least 150, or at least 175, or at least 150, or at least 200, or at least 250, or at least 300, or at least 350 contiguous amino acid residues of any of the amino acid sequence represented disclosed herein. Even small fragments of proteins without biological activity are useful in the present invention, for example, in the preparation of antibodies against the full-length protein or in a screening assay (e.g., a binding assay). Fragments can also be used to construct fusion proteins, for example, where the fusion protein comprises functional domains from two or more different proteins (e.g., a CBD from one protein linked to a CD from another protein). In one embodiment, a homologue has a measurable or detectable biological activity associated with the wild-type protein (e.g., enzymatic activity).

According to the present invention, the term “contiguous” or “consecutive”, with regard to nucleic acid or amino acid sequences described herein, means to be connected in an unbroken sequence. For example, for a first sequence to comprise 30 contiguous (or consecutive) amino acids of a second sequence, means that the first sequence includes an unbroken sequence of 30 amino acid residues that is 100% identical to an unbroken sequence of 30 amino acid residues in the second sequence. Similarly, for a first sequence to have “100% identity” with a second sequence means that the first sequence exactly matches the second sequence with no gaps between nucleotides or amino acids.

In another embodiment, a protein of the present invention, including a homologue, includes a protein having an amino acid sequence that is sufficiently similar to a natural amino acid sequence that a nucleic acid sequence encoding the homologue is capable of hybridizing under moderate, high or very high stringency conditions (described below) to (i.e., with) a nucleic acid molecule encoding the natural protein (i.e., to the complement of the nucleic acid strand encoding the natural amino acid sequence). Preferably, a homologue of a protein of the present invention is encoded by a nucleic acid molecule comprising a nucleic acid sequence that hybridizes under low, moderate, or high stringency conditions to the complement of a nucleic acid sequence that encodes a protein comprising, consisting essentially of, or consisting of, an amino acid sequence represented by any of: SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11, SEQ ID NO:14, SEQ ID NO:17, SEQ ID NO:20, SEQ ID NO:23, SEQ ID NO:26, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38, SEQ ID NO:41, SEQ ID NO:44, SEQ ID NO:47, SEQ ID NO:50, SEQ ID NO:53, SEQ ID NO:56, SEQ ID NO:59, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77, SEQ ID NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, SEQ ID NO:92, or SEQ ID NO:94. Such hybridization conditions are described in detail below.

A nucleic acid sequence complement of nucleic acid sequence encoding a protein of the present invention refers to the nucleic acid sequence of the nucleic acid strand that is complementary to the strand which encodes the protein. It will be appreciated that a double stranded DNA which encodes a given amino acid sequence comprises a single strand DNA and its complementary strand having a sequence that is a complement to the single strand DNA. As such, nucleic acid molecules of the present invention can be either double-stranded or single-stranded, and include those nucleic acid molecules that form stable hybrids under stringent hybridization conditions with a nucleic acid sequence that encodes an amino acid sequence such as SEQ ID NO:2, and/or with the complement of the nucleic acid sequence that encodes an amino acid sequence such as SEQ ID NO:2. Methods to deduce a complementary sequence are known to those skilled in the art. It should be noted that since nucleic acid sequencing technologies are not entirely error-free, the sequences presented herein, at best, represent apparent sequences of the proteins of the present invention.

As used herein, reference to hybridization conditions refers to standard hybridization conditions under which nucleic acid molecules are used to identify similar nucleic acid molecules. Such standard conditions are disclosed, for example, in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Labs Press, 1989. Sambrook et al., ibid., is incorporated by reference herein in its entirety (see specifically, pages 9.31-9.62). In addition, formulae to calculate the appropriate hybridization and wash conditions to achieve hybridization permitting varying degrees of mismatch of nucleotides are disclosed, for example, in Meinkoth et al., 1984, Anal. Biochem. 138, 267-284; Meinkoth et. al., ibid., is incorporated by reference herein in its entirety.

More particularly, moderate stringency hybridization and washing conditions, as referred to herein, refer to conditions which permit isolation of nucleic acid molecules having at least about 70% nucleic acid sequence identity with the nucleic acid molecule being used to probe in the hybridization reaction (i.e. conditions permitting about 30% or less mismatch of nucleotides). High stringency hybridization and washing conditions, as referred to herein, refer to conditions which permit isolation of nucleic acid molecules having at least about 80% nucleic acid sequence identity with the nucleic acid molecule being used to probe in the hybridization reaction (i.e., conditions permitting about 20% or less mismatch of nucleotides). Very high stringency hybridization and washing conditions, as referred to herein, refer to conditions which permit isolation of nucleic acid molecules having at least about 90% nucleic acid sequence identity with the nucleic acid molecule being used to probe in the hybridization reaction (i.e., conditions permitting about 10% or less mismatch of nucleotides). As discussed above, one of skill in the art can use the formulae in Meinkoth et al., ibid. to calculate the appropriate hybridization and wash conditions to achieve these particular levels of nucleotide mismatch. Such conditions will vary, depending on whether DNA:RNA or DNA:DNA hybrids are being formed. Calculated melting temperatures for DNA:DNA hybrids are 10° C. less than for DNA:RNA hybrids. In particular embodiments, stringent hybridization conditions for DNA:DNA hybrids include hybridization at an ionic strength of 6×SSC (0.9 M Na⁺) at a temperature of between about 20° C. and about 35° C. (lower stringency), more preferably, between about 28° C. and about 40° C. (more stringent), and even more preferably, between about 35° C. and about 45° C. (even more stringent), with appropriate wash conditions. In particular embodiments, stringent hybridization conditions for DNA:RNA hybrids include hybridization at an ionic strength of 6×SSC (0.9 M Na⁺) at a temperature of between about 30° C. and about 45° C., more preferably, between about 38° C. and about 50° C., and even more preferably, between about 45° C. and about 55° C., with similarly stringent wash conditions. These values are based on calculations of a melting temperature for molecules larger than about 100 nucleotides, 0% formamide and a G+C content of about 40%. Alternatively, T_(m) can be calculated empirically as set forth in Sambrook et al., supra, pages 9.31 to 9.62. In general, the wash conditions should be as stringent as possible, and should be appropriate for the chosen hybridization conditions. For example, hybridization conditions can include a combination of salt and temperature conditions that are approximately 20-25° C. below the calculated T_(m) of a particular hybrid, and wash conditions typically include a combination of salt and temperature conditions that are approximately 12-20° C. below the calculated T_(m) of the particular hybrid. One example of hybridization conditions suitable for use with DNA:DNA hybrids includes a 2-24 hour hybridization in 6×SSC (50% formamide) at about 42° C., followed by washing steps that include one or more washes at room temperature in about 2×SSC, followed by additional washes at higher temperatures and lower ionic strength (e.g., at least one wash as about 37° C. in about 0.1×-0.5×SSC, followed by at least one wash at about 68° C. in about 0.1×-0.5×SSC).

The minimum size of a protein and/or homologue of the present invention is a size sufficient to have biological activity or, when the protein is not required to have such activity, sufficient to be useful for another purpose associated with a protein of the present invention, such as for the production of antibodies that bind to a naturally occurring protein. In one embodiment, the protein of the present invention is at least 20 amino acids in length, or at least about 25 amino acids in length, or at least about 30 amino acids in length, or at least about 40 amino acids in length, or at least about 50 amino acids in length, or at least about 60 amino acids in length, or at least about 70 amino acids in length, or at least about 80 amino acids in length, or at least about 90 amino acids in length, or at least about 100 amino acids in length, or at least about 125 amino acids in length, or at least about 150 amino acids in length, or at least about 175 amino acids in length, or at least about 200 amino acids in length, or at least about 250 amino acids in length, and so on up to a full length of each protein, and including any size in between in increments of one whole integer (one amino acid). There is no limit, other than a practical limit, on the maximum size of such a protein in that the protein can include a portion of a protein or a full-length protein, plus additional sequence (e.g., a fusion protein sequence), if desired.

The present invention also includes a fusion protein that includes a domain of a protein of the present invention (including a homologue) attached to one or more fusion segments, which are typically heterologous in sequence to the protein sequence (i.e., different than protein sequence). Suitable fusion segments for use with the present invention include, but are not limited to, segments that can: enhance a protein's stability; provide other desirable biological activity; and/or assist with the purification of the protein (e.g., by affinity chromatography). A suitable fusion segment can be a domain of any size that has the desired function (e.g., imparts increased stability, solubility, action or biological activity; and/or simplifies purification of a protein). Fusion segments can be joined to amino and/or carboxyl termini of the domain of a protein of the present invention and can be susceptible to cleavage in order to enable straight-forward recovery of the protein. Fusion proteins are preferably produced by culturing a recombinant cell transfected with a fusion nucleic acid molecule that encodes a protein including the fusion segment attached to either the carboxyl and/or amino terminal end of a domain of a protein of the present invention. Accordingly, proteins of the present invention also include expression products of gene fusions (for example, used to overexpress soluble, active forms of the recombinant protein), of mutagenized genes (such as genes having codon modifications to enhance gene transcription and translation), and of truncated genes (such as genes having membrane binding domains removed to generate soluble forms of a membrane protein, or genes having signal sequences removed which are poorly tolerated in a particular recombinant host).

In one embodiment of the present invention, any of the amino acid sequences described herein can be produced with from at least one, and up to about 20, additional heterologous amino acids flanking each of the C- and/or N-terminal ends of the specified amino acid sequence. The resulting protein or polypeptide can be referred to as “consisting essentially of” the specified amino acid sequence. According to the present invention, the heterologous amino acids are a sequence of amino acids that are not naturally found (i.e., not found in nature, in vivo) flanking the specified amino acid sequence, or that are not related to the function of the specified amino acid sequence, or that would not be encoded by the nucleotides that flank the naturally occurring nucleic acid sequence encoding the specified amino acid sequence as it occurs in the gene, if such nucleotides in the naturally occurring sequence were translated using standard codon usage for the organism from which the given amino acid sequence is derived.

The present invention also provides enzyme combinations that break down lignocellulose material. Such enzyme combinations or mixtures can include a multi-enzyme composition that contains at least one protein of the present invention in combination with one or more additional proteins of the present invention or one or more enzymes or other proteins from other microorganisms, plants, or similar organisms. Synergistic enzyme combinations and related methods are contemplated. The invention includes methods to identify the optimum ratios and compositions of enzymes with which to degrade each lignocellulosic material. These methods entail tests to identify the optimum enzyme composition and ratios for efficient conversion of any lignocellulosic substrate to its constituent sugars. The Examples below include assays that may be used to identify optimum ratios and compositions of enzymes with which to degrade lignocellulosic materials.

Any combination of the proteins disclosed herein is suitable for use in the multi-enzyme compositions of the present invention. Due to the complex nature of most biomass sources, which can contain xylan, lignin, protein, and carbohydrates, among other components, preferred enzyme combinations may contain enzymes with a range of substrate specificities that work together to degrade biomass into fermentable sugars in the most efficient manner. One example of a multi-enzyme complex for lignocellulose saccharification is a mixture of cellobiohydrolase(s), xylanase(s), endoglucanase(s), β-glucosidase(s), β-xylosidase(s), and accessory enzymes. However, it is to be understood that any of the enzymes described specifically herein can be combined with any one or more of the enzymes described herein or with any other available and suitable enzymes, to produce a multi-enzyme composition. The invention is not restricted or limited to the specific exemplary combinations listed below.

In one embodiment, the cellobiohydrolase(s) comprise between about 30% and about 90% or between about 50% and about 70% of the enzymes in the composition, and more preferably, between about 55% and 65%, and more preferably, about 60% of the enzymes in the composition (including any percentage between 50% and 70% in 0.5% increments (e.g. 50%, 50.5%, 51%, etc.).

In one embodiment, the xylanase(s) comprise between about 10% and about 30% of the enzymes in the composition, and more preferably, between about 15% and about 25%, and more preferably, about 20% of the enzymes in the composition (including any percentage between 10% and 30% in 0.5% increments).

In one embodiment, the endoglucanase(s) comprise between about 5% and about 15% of the enzymes in the composition, and more preferably, between about 7% and about 13%, and more preferably, about 10% of the enzymes in the composition (including any percentage between 5% and 15% in 0.5% increments).

In one embodiment, the β-glucosidase(s) comprise between about 1% and about 5% of the enzymes in the composition, and preferably between about 2% and 4%, and more preferably, about 3% of the enzymes in the composition (including any percentage between 1% and 5% in 0.5% increments).

In one embodiment, the β-xylosidase(s) comprise between about 1% and about 3% of the enzymes in the composition, and preferably, between about 1.5% and about 2.5%, and more preferably, about 2% of the enzymes in the composition (including any percentage between 1% and 3% in 0.5% increments.

In one embodiment, the accessory enzymes comprise between about 2% and about 8% of the enzymes in the composition, and preferably, between about 3% and about 7%, and more preferably, about 5% of the enzymes in the composition (including any percentage between 2% and 8% in 0.5% increments.

One particularly preferred example of a multi-enzyme complex for lignocellulose saccharification is a mixture of about 60% cellobiohydrolase(s), about 20% xylanase(s), about 10% endoglucanase(s), about 3% β-glucosidase(s), about 2% β-xylosidase(s) and about 5% accessory enzyme(s).

The multi-enzyme composition may comprise at least one cellobiohydrolase. In some embodiments, the cellobiohydrolase may have an amino acid sequence selected from SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8 SEQ ID NO:11 or a homologue, fusion protein, or fragment thereof that has cellobiohydrolase activity. Compositions comprising at least 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more cellobiohydrolases are contemplated by the invention.

The multi-enzyme composition may comprise at least one endoglucanase. In certain embodiments, the endoglucanase may have an amino acid sequence selected from SEQ ID NO:14, SEQ ID NO:94, SEQ ID NO:17, SEQ ED NO:20 or SEQ ID NO:23 or a homologue, fusion protein, or fragment thereof that has endoglucanase activity. Compositions comprising at least 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more endoglucanases are contemplated by the invention.

The multi-enzyme composition may comprise at least one xylanase. In some embodiments, the xylanase may have an amino acid sequence selected from SEQ ID NO:26, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38 or SEQ ID NO:41 or a homologue, fusion protein, or fragment thereof that has xylanase activity. Compositions comprising at least 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more xylanases are contemplated by the invention.

The multi-enzyme composition may further comprise a β-glucosidase. In one embodiment, the β-glucosidase may have an amino acid sequence of SEQ ID NO:44 or a homologue, fusion protein, or fragment thereof that has β-glucosidase activity. Compositions comprising at least 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more β-glucosidases are contemplated by the invention.

The multi-enzyme composition of may further comprise a hemicellulase. In certain embodiments, the hemicellulase may have an amino acid sequence selected from SEQ ID NO:47, SEQ ID NO:50, SEQ ED NO:53, SEQ ID NO:56, SEQ ID NO:59, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77, SEQ ID NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, SEQ ID NO:92, or a homologue, fusion protein, or fragment thereof that has a hemicellulase activity. Compositions comprising at least 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more hemicellulases are contemplated by the invention.

One or more components of a multi-enzyme composition (other than proteins of the present invention) can be obtained from or derived from a microbial, plant, or other source or combination thereof, and will contain enzymes capable of degrading lignocellulosic material. Examples of enzymes included in the multi-enzyme compositions of the invention include cellulases, hemicellulases (such as xylanases, including endoxylanases, exoxylanase, and β-xylosidase), ligninases, amylases, glucuronidases, proteases, esterases (including ferulic acid esterase), lipases, glucosidases (such as β-glucosidase), glucomannanases, and xylogluconases.

While the multi-enzyme composition may contain many types of enzymes, mixtures comprising enzymes that increase or enhance sugar release from biomass are preferred, including hemicellulases. In one embodiment, the hemicellulase is selected from a xylanase, an arabinofuranosidase, an acetyl xylan esterase, a glucuronidase, an endo-galactanase, a mannanase, an endo-arabinase, an exo-arabinase, an exo-galactanase, a ferulic acid esterase, a galactomannanase, a xylogluconase, or mixtures of any of these. In particular, the enzymes can include glucoamylase, β-xylosidase and/or β-glucosidase. The enzymes of the multi-enzyme composition can be provided by a variety of sources. In one embodiment, the enzymes can be produced by a growing microorganisms or plants which produce the enzymes naturally or by virtue of being genetically modified to express the enzyme or enzymes. In another embodiment, at least one enzyme of the multi-enzyme composition is a commercially available enzyme.

In some embodiments, the multi-enzyme compositions comprise an accessory enzyme. An accessory enzyme is any additional enzyme capable of hydrolyzing lignocellulose or enhancing or promoting the hydrolysis of lignocellulose, wherein the accessory enzyme is typically provided in addition to a core enzyme or core set of enzymes. An accessory enzyme can have the same or similar function or a different function as an enzyme or enzymes in the core set of enzymes. These enzymes have been described elsewhere herein, and can generally include cellulases, xylanases, ligninases, amylases, lipidases, or glucuronidases, for example. Accessory enzymes can include enzymes that when contacted with biomass in a reaction, allow for an increase in the activity of enzymes (e.g., hemicellulases) in the multi-enzyme composition. An accessory enzyme or enzyme mix may be composed of enzymes from (1) commercial suppliers; (2) cloned genes expressing enzymes; (3) complex broth (such as that resulting from growth of a microbial strain in media, wherein the strains secrete proteins and enzymes into the media); (4) cell lysates of strains grown as in (3); and, (5) plant material expressing enzymes capable of degrading lignocellulose. In some embodiments, the accessory enzyme is a glucoamylase, a pectinase, or a ligninase.

As used herein, a ligninase is an enzyme that can hydrolyze or break down the structure of lignin polymers, including lignin peroxidases, manganese peroxidases, laccases, and other enzymes described in the art known to depolymerize or otherwise break lignin polymers. Also included are enzymes capable of hydrolyzing bonds formed between hemicellulosic sugars (notably arabinose) and lignin.

In one embodiment, the multi-enzyme composition comprises the enzyme CBH Ia (SEQ ID NO:2), a biologically active (e.g., has enzyme activity) homologue thereof, or a fragment comprising, consisting essentially of, or consisting of the CD thereof. In another embodiment, the multi-enzyme composition comprises the enzyme CBH IIb (SEQ ID NO:11), a biologically active homologue thereof, or a fragment comprising, consisting essentially of or consisting of the CD thereof. In another embodiment, the multi-enzyme composition comprises the enzyme EG II (SEQ ID NO:94), a biologically active homologue thereof, or a fragment comprising, consisting essentially of, or consisting of the CD thereof. In a further embodiment, the multi-enzyme composition comprises the enzyme Xyl 2 (SEQ ID NO:29), a biologically active homologue thereof, or a fragment comprising, consisting essentially of, or consisting of the CD thereof. In yet another embodiment, the multi-enzyme composition comprises the enzyme β-glucosidase (SEQ ID NO:44), a biologically active homologue thereof, or a fragment comprising, consisting essentially of, or consisting of the CD thereof. In certain embodiments, the multi-enzyme composition comprises any combination of the enzymes listed above. In other embodiments, the multi-enzyme composition comprises at least one of the enzymes listed above in combination with a β-xylosidase enzyme.

In one embodiment, the multi-enzyme composition comprises CBH Ia (SEQ ID NO:2), CBH IIb (SEQ ID NO:11), EG II (SEQ ID NO:94), the CD of Xyl 2 (SEQ ID NO:29) and the CD of β-glucosidase (SEQ ID NO:44). This preferred enzyme combination may further comprise a β-xylosidase enzyme. One of skill in the art will appreciate, however, that any enzyme in the combinations described above may be replaced with an enzyme exhibiting a similar substrate specificity. Further, the optimal enzyme combination for a particular use (e.g., for degradation of a biomass derived from a specific source) can be determined by one of skill in the art using routine experimentation and assays known in the art, such as those disclosed herein.

In one embodiment, the multi-enzyme composition comprises the enzyme CBH Ib (SEQ ID NO:5), a biologically active homologue thereof, or a fragment comprising, consisting essentially of, or consisting of the CD thereof. In an additional embodiment, the multi-enzyme composition comprises the enzyme EG V (SEQ ID NO:20), a biologically active homologue thereof, or a fragment comprising, consisting essentially of, or consisting of the CD thereof. In still another embodiment, the multi-enzyme composition comprises the enzyme Xyl 1 (SEQ ID NO:26), a biologically active homologue thereof, or a fragment comprising, consisting essentially of, or consisting of the CD thereof. In further embodiments, the multi-enzyme composition comprises the enzyme arabinogalactanase (SEQ ID NO:47), a biologically active homologue thereof, or a fragment comprising, consisting essentially of, or consisting of the CD thereof. In certain embodiments, the multi-enzyme composition comprises any combination of the enzymes listed above. In other embodiments, the multi-enzyme composition comprises at least one of the enzymes listed above in combination with at least one accessory enzyme such as, for example, α-L-arabinofuranosidase.

In a preferred embodiment, the multi-enzyme composition comprises the CD of CBH Ib (SEQ ID NO:5), the CD of EG V (SEQ ID NO:20), the CD of Xyl 1 (SEQ ID NO:26) and the CD of arabinogalactanase (SEQ ID NO:47). This preferred enzyme combination may further comprise at least one accessory enzyme. One of skill in the art will appreciate, however, that any enzyme in the combinations described above may be replaced with an enzyme exhibiting a similar substrate specificity. Further, the optimal enzyme combination for a particular use (e.g., for degradation of a biomass derived from a specific source) can be determined by one of skill in the art using routine experimentation and assays known in the art, such as those disclosed herein.

The multi-enzyme compositions, in some embodiments, comprise a biomass comprising microorganisms or a crude fermentation product of microorganisms. A crude fermentation product refers to the fermentation broth which has been separated from the microorganism biomass (by filtration, for example). In general, the microorganisms are grown in fermentors, optionally centrifuged or filtered to remove biomass, and optionally concentrated, formulated, and dried to produce an enzyme(s) or a multi-enzyme composition that is a crude fermentation product. In other embodiments, enzyme(s) or multi-enzyme compositions produced by the microorganism (including a genetically modified microorganism as described below) are subjected to one or more purification steps, such as ammonium sulfate precipitation, chromatography, and/or ultrafiltration, which result in a partially purified or purified enzyme(s). If the microorganism has been genetically modified to express the enzyme(s), the enzyme(s) will include recombinant enzymes. If the genetically modified microorganism also naturally expresses the enzyme(s) or other enzymes useful for lignocellulosic saccharification, the enzyme(s) may include both naturally occurring and recombinant enzymes.

Another embodiment of the present invention relates to a composition comprising at least about 500 ng, and preferably at least about 1 μg, and more preferably at least about 5 μg, and more preferably at least about 10 μg, and more preferably at least about 25 μg, and more preferably at least about 50 μg, and more preferably at least about 75 μg, and more preferably at least about 100 μg, and more preferably at least about 250 μg, and more preferably at least about 500 μg, and more preferably at least about 750 μg, and more preferably at least about 1 mg, and more preferably at least about 5 mg, of an isolated protein comprising any of the proteins or homologues or fragments thereof discussed herein. Such a composition of the present invention may include any carrier with which the protein is associated by virtue of the protein preparation method, a protein purification method, or a preparation of the protein for use in any method according to the present invention. For example, such a carrier can include any suitable buffer, extract, or medium that is suitable for combining with the protein of the present invention so that the protein can be used in any method described herein according to the present invention.

In one embodiment of the invention, one or more enzymes of the invention is bound to a solid support, i.e., an immobilized enzyme. As used herein, an immobilized enzyme includes immobilized isolated enzymes, immobilized microbial cells which contain one or more enzymes of the invention, other stabilized intact cells that produce one or more enzymes of the invention, and stabilized cell/membrane homogenates. Stabilized intact cells and stabilized cell/membrane homogenates include cells and homogenates from naturally occurring microorganisms expressing the enzymes of the invention and preferably, from genetically modified microorganisms as disclosed elsewhere herein. Thus, although methods for immobilizing enzymes are discussed below, it will be appreciated that such methods are equally applicable to immobilizing, microbial cells and in such an embodiment, the cells can be lysed, if desired.

A variety of methods for immobilizing an enzyme are disclosed in Industrial Enzymology 2nd Ed. Godfrey, T. and West. S. Eds., Stockton Press, New York, N.Y., 1996, pp. 267-272; Immobilized Enzymes, Chibata, I. Ed., Halsted Press, New York, N.Y., 1978; Enzymes and Immobilized Cells in Biotechnology, Laskin, A. Ed., Benjamin/Cummings Publishing Co., Inc., Menlo Park, Calif., 1985; and Applied Biochemistry and Bioengineering, Vol. 4, Chibata, I. and Wingard, Jr., L. Eds, Academic Press, New York, N.Y., 1983, which are incorporated herein in their entirety.

Briefly, a solid support refers to any solid organic, biopolymer or inorganic supports that can form a bond with an enzyme without significantly effecting the activity of the enzyme. Exemplary organic solid supports include polymers such as polystyrene, nylon, phenol-formaldehyde resins, acrylic copolymers (e.g., polyacrylamide), stabilized intact whole cells, and stabilized crude whole cell/membrane homogenates. Exemplary biopolymer supports include cellulose, polydextrans (e.g., Sephadex®), agarose, collagen and chitin. Exemplary inorganic supports include glass beads (porous and nonporous), stainless steel, metal oxides (e.g., porous ceramics such as ZrO₂, TiO₂, Al₂O₃, and NiO) and sand. In one embodiment, the solid support is selected from the group consisting of stabilized intact cells and/or crude cell homogenates (e.g., produced from the microbial host cells expressing recombinant enzymes, alone or in combination with natural enzymes). Preparation of such supports requires a minimum of handling and cost. Additionally, such supports provide excellent stability of the enzyme.

Stabilized intact cells and/or cell/membrane homogenates can be produced, for example, by using bifunctional crosslinkers (e.g., glutaraldehyde) to stabilize cells and cell homogenates. In both the intact cells and the cell membranes, the cell wall and membranes act as immobilizing supports. In such a system, integral membrane proteins are in the “best” lipid membrane environment. Whether starting with intact cells or homogenates, in this system the cells are either no longer “alive” or “metabolizing”, or alternatively, are “resting” (i.e., the cells maintain metabolic potential and active enzyme, but under the culture conditions are not growing); in either case, the immobilized cells or membranes serve as biocatalysts.

An enzyme of the invention can be bound to a solid support by a variety of methods including adsorption, cross-linking (including covalent bonding), and entrapment. Adsorption can be through van del Waal's forces, hydrogen bonding, ionic bonding, or hydrophobic binding. Exemplary solid supports for adsorption immobilization include polymeric adsorbents and ion-exchange resins. Solid supports in a bead form are particularly well-suited. The particle size of an adsorption solid support can be selected such that the immobilized enzyme is retained in the reactor by a mesh filter while the substrate is allowed to flow through the reactor at a desired rate. With porous particulate supports it is possible to control the adsorption process to allow enzymes or cells to be embedded within the cavity of the particle, thus providing protection without an unacceptable loss of activity.

Cross-linking of an enzyme to a solid support involves forming a chemical bond between a solid support and the enzyme. It will be appreciated that although cross-linking generally involves linking the enzyme to a solid support using an intermediary compound, it is also possible to achieve a covalent bonding between the enzyme and the solid support directly without the use of an intermediary compound. Cross-linking commonly uses a bifunctional or multifunctional reagent to activate and attach a carboxyl group, amino group, sulfur group, hydroxy group or other functional group of the enzyme to the solid support. The term “activate” refers to a chemical transformation of a functional group which allows a formation of a bond at the functional group. Exemplary amino group activating reagents include water-soluble carbodiimides, glutaraldehyde, cyanogen bromide, N-hydroxysuccinimide esters, triazines, cyanuric chloride, and carbonyl diimidazole. Exemplary carboxyl group activating reagents include water-soluble carbodiimides, and N-ethyl-5-phenylisoxazolium-3-sulfonate. Exemplary tyrosyl group activating reagents include diazonium compounds. And exemplary sulfhydryl group activating reagents include dithiobis-5,5′-(2-nitrobenzoic acid), and glutathione-2-pyridyl disulfide. Systems for covalently linking an enzyme directly to a solid support include Eupergit®, a polymethacrylate bead support available from Rohm Pharma (Darmstadt, Germany), kieselguhl (Macrosorbs), available from Sterling Organics, kaolinite available from English China Clay as “Biofix” supports, silica gels which can be activated by silanization, available from W.R. Grace, and high-density alumina, available from UOP (Des Plains, Ill.).

Entrapment can also be used to immobilize an enzyme. Entrapment of an enzyme involves formation of, inter alia, gels (using organic or biological polymers), vesicles (including microencapsulation), semipermeable membranes or other matrices. Exemplary materials used for entrapment of an enzyme include collagen, gelatin, agar, cellulose triacetate, alginate, polyacrylamide, polystyrene, polyurethane, epoxy resins, carrageenan, and egg albumin. Some of the polymers, in particular cellulose triacetate, can be used to entrap the enzyme as they are spun into a fiber. Other materials such as polyacrylamide gels can be polymerized in solution to entrap the enzyme. Still other materials such as polyglycol oligomers that are functionalized with polymerizable vinyl end groups can entrap enzymes by forming a cross-linked polymer with UV light illumination in the presence of a photosensitizer.

Further embodiments of the present invention include nucleic acid molecules that encode a protein of the present invention, as well as homologues or fragments of such nucleic acid molecules. A nucleic acid molecule of the present invention includes a nucleic acid molecule comprising, consisting essentially of, or consisting of, a nucleic acid sequence encoding any of the isolated proteins disclosed herein, including a fragment or a homologue of such proteins, described above. Nucleic acid molecules can include a nucleic acid sequence that encodes a fragment of a protein that does not have biological activity, and can also include portions of a gene or polynucleotide encoding the protein that are not part of the coding region for the protein (e.g., introns or regulatory regions of a gene encoding the protein). Nucleic acid molecules can include a nucleic acid sequence that is useful as a probe or primer (oligonucleotide sequences).

In one embodiment, a nucleic molecule of the present invention includes a nucleic acid molecule comprising, consisting essentially of or consisting of, a nucleic acid sequence represented by SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:12, SEQ ID SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:79, SEQ ID NO:90, SEQ ID NO:91, SEQ ID NO:93, or fragments or homologues thereof. Preferably, the nucleic acid sequence encodes a protein (including fragments and homologues thereof) useful in the invention, or encompasses useful oligonucleotides or complementary nucleic acid sequences.

In one embodiment, a nucleic molecule of the present invention includes a nucleic acid molecule comprising, consisting essentially of, or consisting of, a nucleic acid sequence encoding an amino acid sequence represented by SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11, SEQ ID NO:14, SEQ ID NO:17, SEQ ID NO:20, SEQ ID NO:23, SEQ ID NO:26, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38, SEQ ID NO:41, SEQ ID NO:44, SEQ ID NO:47, SEQ ID NO:50, SEQ ID NO:53, SEQ ID NO:56, SEQ ID NO:59, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77, SEQ ID NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, SEQ ID NO:92, SEQ ID NO:94 or fragments or homologues thereof. Preferably, the nucleic acid sequence encodes a protein (including fragments and homologues thereof) useful in the invention, or encompasses useful oligonucleotides or complementary nucleic acid sequences.

In one embodiment, such nucleic acid molecules include isolated nucleic acid molecules that hybridize under moderate stringency conditions, and more preferably under high stringency conditions, and even more preferably under very high stringency conditions, as described above, with the complement of a nucleic acid sequence encoding a protein of the present invention (i.e., including naturally occurring allelic variants encoding a protein of the present invention). Preferably, an isolated nucleic acid molecule encoding a protein of the present invention comprises a nucleic acid sequence that hybridizes under moderate, high, or very high stringency conditions to the complement of a nucleic acid sequence that encodes a protein comprising an amino acid sequence represented by SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11, SEQ ID NO:14, SEQ ID NO:17, SEQ ID NO:20, SEQ ID NO:23, SEQ ID NO:26, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38, SEQ ID NO:41, SEQ ID NO:44, SEQ ID NO:47, SEQ ID NO:50, SEQ ID NO:53, SEQ ID NO:56, SEQ ID NO:59, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77, SEQ ID NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, SEQ ID NO:92, or SEQ ID NO:94.

In accordance with the present invention, an isolated nucleic acid molecule is a nucleic acid molecule (polynucleotide) that has been removed from its natural milieu (i.e., that has been subject to human manipulation) and can include. DNA, RNA, or derivatives of either DNA or RNA, including cDNA. As such, “isolated” does not reflect the extent to which the nucleic acid molecule has been purified. Although the phrase “nucleic acid molecule” primarily refers to the physical nucleic acid molecule, and the phrase “nucleic acid sequence” primarily refers to the sequence of nucleotides on the nucleic acid molecule, the two phrases can be used interchangeably, especially with respect to a nucleic acid molecule, or a nucleic acid sequence, being capable of encoding a protein. An isolated nucleic acid molecule of the present invention can be isolated from its natural source or produced using recombinant DNA technology (e.g., polymerase chain reaction (PCR) amplification, cloning) or chemical synthesis. Isolated nucleic acid molecules can include, for example, genes, natural allelic variants of genes, coding regions or portions thereof, and coding and/or regulatory regions modified by nucleotide insertions, deletions, substitutions, and/or inversions in a manner such that the modifications do not substantially interfere with the nucleic acid molecule's ability to encode a protein of the present invention or to form stable hybrids under stringent conditions with natural gene isolates. An isolated nucleic acid molecule can include degeneracies. As used herein, nucleotide degeneracy refers to the phenomenon that one amino acid can be encoded by different nucleotide codons. Thus, the nucleic acid sequence of a nucleic acid molecule that encodes a protein of the present invention can vary due to degeneracies. It is noted that a nucleic acid molecule of the present invention is not required to encode a protein having protein activity. A nucleic acid molecule can encode a truncated, mutated or inactive protein, for example. In addition, nucleic acid molecules of the invention are useful as probes and primers for the identification, isolation and/or purification of other nucleic acid molecules. If the nucleic acid molecule is an oligonucleotide, such as a probe or primer, the oligonucleotide preferably ranges from about 5 to about 50 or about 500 nucleotides, more preferably from about 10 to about 40 nucleotides, and most preferably from about 15 to about 40 nucleotides in length.

According to the present invention, reference to a gene includes all nucleic acid sequences related to a natural (i.e. wild-type) gene, such as regulatory regions that control production of the protein encoded by that gene (such as, but not limited to, transcription, translation or post-translation control regions) as well as the coding region itself. In another embodiment, a gene can be a naturally occurring allelic variant that includes a similar but not identical sequence to the nucleic acid sequence encoding a given protein. Allelic variants have been previously described above. The phrases “nucleic acid molecule” and “gene” can be used interchangeably when the nucleic acid molecule comprises a gene as described above.

Preferably, an isolated nucleic acid molecule of the present invention is produced using recombinant DNA technology (e.g., polymerase chain reaction (PCR) amplification, cloning, etc.) or chemical synthesis. Isolated nucleic acid molecules include any nucleic acid molecules and homologues thereof that are part of a gene described herein and/or that encode a protein described herein, including, but not limited to, natural allelic variants and modified nucleic acid molecules (homologues) in which nucleotides have been inserted, deleted, substituted, and/or inverted in such a manner that such modifications provide the desired effect on protein biological activity or on the activity of the nucleic acid molecule. Allelic variants and protein homologues (e.g., proteins encoded by nucleic acid homologues) have been discussed in detail above.

A nucleic acid molecule homologue (i.e., encoding a homologue of a protein of the present invention) can be produced using a number of methods known to those skilled in the art (see, for example, Sambrook et al.). For example, nucleic acid molecules can be modified using a variety of techniques including, but not limited to, by classic mutagenesis and recombinant DNA techniques (e.g., site-directed mutagenesis, chemical treatment, restriction enzyme cleavage, ligation of nucleic acid fragments and/or PCR amplification), or synthesis of oligonucleotide mixtures and ligation of mixture groups to “build” a mixture of nucleic acid molecules and combinations thereof. Another method for modifying a recombinant nucleic acid molecule encoding a protein is gene shuffling (i.e., molecular breeding) (See, for example. U.S. Pat. No. 5,605,793 to Stemmer; Minshull and Stemmer; 1999, Curr. Opin. Chem. Biol. 3:284-290; Stemmer, 1994, P.N.A.S. USA 91:10747-10751, all of which are incorporated herein by reference in their entirety). This technique can be used to efficiently introduce multiple simultaneous changes in the protein. Nucleic acid molecule homologues can be selected by hybridization with a gene or polynucleotide, or by screening for the function of a protein encoded by a nucleic acid molecule (i.e., biological activity).

The minimum size of a nucleic acid molecule of the present invention is a size sufficient to encode a protein (including a fragment or homologue of a full-length protein) having biological activity, sufficient to encode a protein comprising at least one epitope which binds to an antibody, or sufficient to form a probe or oligonucleotide primer that is capable of forming a stable hybrid with the complementary sequence of a nucleic acid molecule encoding a natural protein (e.g., under moderate, high, or high stringency conditions). As such, the size of the nucleic acid molecule encoding such a protein can be dependent on nucleic acid composition and percent homology or identity between the nucleic acid molecule and complementary sequence as well as upon hybridization conditions per se (e.g., temperature, salt concentration, and formamide concentration). The minimal size of a nucleic acid molecule that is used as an oligonucleotide primer or as a probe is typically at least about 12 to about 15 nucleotides in length if the nucleic acid molecules are GC-rich and at least about 15 to about 18 bases in length if they are AT-rich. There is no limit, other than a practical limit, on the maximal size of a nucleic acid molecule of the present invention, in that the nucleic acid molecule can include a portion of a protein encoding sequence, a nucleic acid sequence encoding a full-length protein (including a gene), including any length fragment between about 20 nucleotides and the number of nucleotides that make up the full length cDNA encoding a protein, in whole integers (e.g., 20, 21, 22, 23, 24, 25 . . . nucleotides), or multiple genes, or portions thereof.

The phrase “consisting essentially of”, when used with reference to a nucleic acid sequence herein, refers to a nucleic acid sequence encoding a specified amino acid sequence that can be flanked by from at least one, and up to as many as about 60, additional heterologous nucleotides at each of the 5′ and/or the 3′ end of the nucleic acid sequence encoding the specified amino acid sequence. The heterologous nucleotides are not naturally found (i.e., not found in nature, in vivo) flanking the nucleic acid sequence encoding the specified amino acid sequence as it occurs in the natural gene or do not encode a protein that imparts any additional function to the protein or changes the function of the protein having the specified amino acid sequence.

In one embodiment, the polynucleotide probes or primers of the invention are conjugated to detectable markers. Detectable labels suitable for use in the present invention include any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Useful labels in the present invention include biotin for staining with labeled streptavidin conjugate, magnetic beads (e.g., Dynabeads™), fluorescent dyes (e.g., fluorescein, texas red, rhodamine, green fluorescent protein, and the like), radiolabels (e.g., ³H, ¹²⁵I, ³⁵S, ¹⁴C, or ³²P), enzymes (e.g., horse radish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and colorimetric labels such as colloidal gold or colored glass or plastic (e.g., polystyrene, polypropylene, latex, etc.) beads. Preferably, the polynucleotide probes are immobilized on a substrate such as: artificial membranes, organic supports, biopolymer supports and inorganic supports.

One embodiment of the present invention relates to a recombinant nucleic acid molecule which comprises the isolated nucleic acid molecule described above which is operatively linked to at least one expression control sequence. More particularly, according to the present invention, a recombinant nucleic acid molecule typically comprises a recombinant vector and any one or more of the isolated nucleic acid molecules as described herein. According to the present invention, a recombinant vector is an engineered (i.e., artificially produced) nucleic acid molecule that is used as a tool for manipulating a nucleic acid sequence of choice and/or for introducing such a nucleic acid sequence into a host cell. The recombinant vector is therefore suitable for use in cloning, sequencing, and/or otherwise manipulating the nucleic acid sequence of choice, such as by expressing and/or delivering the nucleic acid sequence of choice into a host cell to form a recombinant cell. Such a vector typically contains heterologous nucleic acid sequences, that is, nucleic acid sequences that are not naturally found adjacent to nucleic acid sequence to be cloned or delivered, although the vector can also contain regulatory nucleic acid sequences (e.g., promoters, untranslated regions) which are naturally found adjacent to nucleic acid sequences of the present invention or which are useful for expression of the nucleic acid molecules of the present invention (discussed in detail below). The vector can be either RNA or DNA, either prokaryotic or eukaryotic, and typically is a plasmid. The vector can be maintained as an extrachromosomal element (e.g., a plasmid) or it can be integrated into the chromosome of a recombinant host cell, although it is preferred if the vector remain separate from the genome for most applications of the invention. The entire vector can remain in place within a host cell, or under certain conditions, the plasmid DNA can be deleted, leaving behind the nucleic acid molecule of the present invention. An integrated nucleic acid molecule can be under chromosomal promoter control, under native or plasmid promoter control, or under a combination of several promoter controls. Single or multiple copies of the nucleic acid molecule can be integrated into the chromosome. A recombinant vector of the present invention can contain at least one selectable marker.

In one embodiment, a recombinant vector used in a recombinant nucleic acid molecule of the present invention is an expression vector. As used herein, the phrase “expression vector” is used to refer to a vector that is suitable for production of an encoded product (e.g., a protein of interest, such as an enzyme of the present invention). In this embodiment, a nucleic acid sequence encoding the product to be produced (e.g., the protein or homologue thereof) is inserted into the recombinant vector to produce a recombinant nucleic acid molecule. The nucleic acid sequence encoding the protein to be produced is inserted into the vector in a manner that operatively links the nucleic acid sequence to regulatory sequences in the vector which enable the transcription and translation of the nucleic acid sequence within the recombinant host cell.

Typically, a recombinant nucleic acid molecule includes at least one nucleic acid molecule of the present invention operatively linked to one or more expression control sequences (e.g., transcription control sequences, or translation control sequences). As used herein, the phrase “recombinant molecule” or “recombinant nucleic acid molecule” primarily refers to a nucleic acid molecule or nucleic acid sequence operatively linked to a transcription control sequence, but can be used interchangeably with the phrase “nucleic acid molecule”, when such nucleic acid molecule is a recombinant molecule as discussed herein. According to the present invention, the phrase “operatively linked” refers to linking a nucleic acid molecule to an expression control sequence in a manner such that the molecule is able to be expressed when transfected (i.e., transformed, transduced, transfected, conjugated or conduced) into a host cell. Transcription control sequences are sequences which control the initiation, elongation, or termination of transcription. Particularly important transcription control sequences are those which control transcription initiation, such as promoter, enhancer, operator and repressor sequences. Suitable transcription control sequences include any transcription control sequence that can function in a host cell or organism into which the recombinant nucleic acid molecule is to be introduced.

Recombinant nucleic acid molecules of the present invention can also contain additional regulatory sequences, such as translation regulatory sequences, origins of replication, and other regulatory sequences that are compatible with the recombinant cell. In one embodiment, a recombinant molecule of the present invention, including those which are integrated into the host cell chromosome, also contains secretory signals (i.e., signal segment nucleic acid sequences) to enable an expressed protein to be secreted from the cell that produces the protein. Suitable signal segments include a signal segment that is naturally associated with the protein to be expressed or any heterologous signal segment capable of directing the secretion of the protein according to the present invention. In another embodiment, a recombinant molecule of the present invention comprises a leader sequence to enable an expressed protein to be delivered to and inserted into the membrane of a host cell. Suitable leader sequences include a leader sequence that is naturally associated with the protein, or any heterologous leader sequence capable of directing the delivery and insertion of the protein to the membrane of a cell.

According to the present invention, the term “transfection” is generally used to refer to any method by which an exogenous nucleic acid molecule (i.e., a recombinant nucleic acid molecule) can be inserted into a cell. The term “transformation” can be used interchangeably with the term “transfection” when such term is used to refer to the introduction of nucleic acid molecules into microbial cells or plants and describes an inherited change due to the acquisition of exogenous nucleic acids by the microorganism that is essentially synonymous with the term “transfection.” Transfection techniques include, but are not limited to, transformation, particle bombardment, electroporation, microinjection, lipofection, adsorption, infection and protoplast fusion.

One or more recombinant molecules of the present invention can be used to produce an encoded product (e.g., a protein) of the present invention. In one embodiment, an encoded product is produced by expressing a nucleic acid molecule as described herein under conditions effective to produce the protein. A preferred method to produce an encoded protein is by transfecting a host cell with one or more recombinant molecules to form a recombinant cell. Suitable host cells to transfect include, but are not limited to, any bacterial, fungal (e.g., filamentous fungi or yeast), plant, insect, or animal cell that can be transfected. Host cells can be either untransfected cells or cells that are already transfected with at least one other recombinant nucleic acid molecule.

Suitable cells (e.g., a host cell or production organism) include any microorganism (e.g., a bacterium, a protist, an alga, a fungus, or other microbe), and is preferably a bacterium, a yeast or a filamentous fungus. Suitable bacterial genera include, but are not limited to, Escherichia, Bacillus, Lactobacillus, Pseudomonas and Streptomyces. Suitable bacterial species include, but are not limited to, Escherichia coli, Bacillus subtilis, Bacillus licheniformis, Lactobacillus brevis, Pseudomonas aeruginosa and Streptomyces lividans. Suitable genera of yeast include, but are not limited to Saccharomyces, Schizosaccharomyces, Candida, Hansenula, Pichia, Kluyveromyces, and Phaffia. Suitable yeast species include, but are not limited to, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans, Hansenula polymorpha, Pichia pastoris, P. canadensis, Kluyveromyces marxianus and Phaffia rhodozyma.

Suitable fungal genera include, but are not limited to, Chrysosporium, Thielavia, Neurospora, Aureobasidium, Filibasidium, Piromyces, Corynascus, Cryplococcus, Acrernoniurn, Tolypocladium, Scytalidium, Schizophyllum, Sporotrichum, Penicillium, Gibberella, Myceliophthora, Mucor, Aspergillus, Fusarium, Humicola, and Trichoderma, and anamorphs and teleomorphs thereof. Suitable fungal species include, but are not limited to, Aspergillus niger, Aspergillus nidulans, Aspergillus japonicus, Absidia coerulea, Rhizopus oryzae, Chrysosporium lucknowense, Neurospora crassa, Neurospora intermedia, Trichoderma reesei, Penicillium canescens, Penicillium solitum, Penicillium funiculosum, and Talaromyces flavus. In one embodiment, the host cell is a fungal cell of the species Chrysosporium lucknowense. In one embodiment, the host cell is a fungal cell of Strain C1 (VKM F-3500-D) or a mutant strain derived therefrom (e.g., UV13-6 (Accession No. VKM F-3632 D); NG7C-19 (Accession No. VKM F-3633 D); or UV18-25 (VKM F-3631D)). Host cells can be either untransfected cells or cells that are already transfected with at least one other recombinant nucleic acid molecule. Additional embodiments of the present invention include any of the genetically modified cells described herein.

In one embodiment, one or more protein(s) expressed by an isolated nucleic acid molecule of the present invention are produced by culturing a cell that expresses the protein (i.e., a recombinant cell or recombinant host cell) under conditions effective to produce the protein. In some instances, the protein may be recovered, and in others, the cell may be harvested in whole, either of which can be used in a composition.

Microorganisms used in the present invention (including recombinant host cells or genetically modified microorganisms) are cultured in an appropriate fermentation medium. An appropriate, or effective, fermentation medium refers to any medium in which a cell of the present invention, including a genetically modified microorganism (described below), when cultured, is capable of expressing enzymes useful in the present invention and/or of catalyzing the production of sugars from lignocellulosic biomass. Such a medium is typically an aqueous medium comprising assimilable carbon, nitrogen and phosphate sources. Such a medium can also include appropriate salts, minerals, metals and other nutrients. Microorganisms and other cells of the present invention can be cultured in conventional fermentation bioreactors. The microorganisms can be cultured by any fermentation process which includes, but is not limited to, batch, fed-batch, cell recycle, and continuous fermentation. The fermentation of microorganisms such as fungi may be carried out in any appropriate reactor, using methods known to those skilled in the art. For example, the fermentation may be carried out for a period of 1 to 14 days, or more preferably between about 3 and 10 days. The temperature of the medium is typically maintained between about 25 and 50° C., and more preferably between 28 and 40° C. The pH of the fermentation medium is regulated to a pH suitable for growth and protein production of the particular organism. The fermentor can be aerated in order to supply the oxygen necessary for fermentation and to avoid the excessive accumulation of carbon dioxide produced by fermentation. In addition, the aeration helps to control the temperature and the moisture of the culture medium. In general the fungal strains are grown in fermentors, optionally centrifuged or filtered, to remove biomass, and optionally concentrated, formulated, and dried to produce an enzyme(s) or a multi-enzyme composition that is a crude fermentation product. Particularly suitable conditions for culturing filamentous fungi are described, for example, in U.S. Pat. No. 6,015,707 and U.S. Pat. No. 6,573,086, supra:

Depending on the vector and host system used for production, resultant proteins of the present invention may either remain within the recombinant cell; be secreted into the culture medium; be secreted into a space between two cellular membranes; or be retained on the outer surface of a cell membrane. The phrase “recovering the protein” refers to collecting the whole culture medium containing the protein and need not imply additional steps of separation or purification. Proteins produced according to the present invention can be purified using a variety of standard protein purification techniques, such as, but not limited to, affinity chromatography, ion exchange chromatography, filtration, electrophoresis, hydrophobic interaction chromatography, gel filtration chromatography, reverse phase chromatography, concanavalin A chromatography, chromatofocusing and differential solubilization.

Proteins of the present invention are preferably retrieved, obtained, and/or used in “substantially pure” form. As used herein, “substantially pure” refers to a purity that allows for the effective use of the protein in any method according to the present invention. For a protein to be useful in any of the methods described herein or in any method utilizing enzymes of the types described herein according to the present invention, it is substantially free of contaminants, other proteins and/or chemicals that might interfere or that would interfere with its use in a method disclosed by the present invention (e.g., that might interfere with enzyme activity), or that at least would be undesirable for inclusion with a protein of the present invention (including homologues) when it is used in a method disclosed by the present invention (described in detail below). Preferably, a “substantially pure” protein, as referenced herein, is a protein that can be produced by any method (i.e., by direct purification from a natural source, recombinantly, or synthetically), and that has been purified from other protein components such that the protein comprises at least about 80% weight/weight of the total protein in a given composition (e.g., the protein of interest is about 80% of the protein in a solution/composition/buffer), and more preferably, at least about 85%, and more preferably at least about 90%, and more preferably at least about 91%, and more preferably at least about 92%, and more preferably at least about 93%, and more preferably at least about 94%, and more preferably at least about 95%, and more preferably at least about 96%, and more preferably at least about 97%, and more preferably at least about 98%, and more preferably at least about 99%, weight/weight of the total protein in a given composition.

It will be appreciated by one skilled in the art that use of recombinant DNA technologies can improve control of expression of transfected nucleic acid molecules by manipulating, for example, the number of copies of the nucleic acid molecules within the host cell, the efficiency with which those nucleic acid molecules are transcribed, the efficiency with which the resultant transcripts are translated, and the efficiency of post-translational modifications. Additionally, the promoter sequence might be genetically engineered to improve the level of expression as compared to the native promoter. Recombinant techniques useful for controlling the expression of nucleic acid molecules include, but are not limited to, integration of the nucleic acid molecules into one or more host cell chromosomes, addition of vector stability sequences to plasmids, substitutions or modifications of transcription control signals (e.g., promoters, operators, enhancers), substitutions or modifications of translational control signals (e.g., ribosome binding sites), modification of nucleic acid molecules to correspond to the codon usage of the host cell, and deletion of sequences that destabilize transcripts.

Another aspect of the present invention relates to a genetically modified microorganism that has been transfected with one or more nucleic acid molecules of the present invention. As used herein, a genetically modified microorganism can include a genetically modified bacterium, yeast, filamentous fungus, or other microbe. Such a genetically modified microorganism has a genome which is modified (i.e., mutated or changed) from its normal (i.e., wild-type or naturally occurring) form such that the desired result is achieved (i.e., increased or modified activity and/or production of at least one an enzyme or a multi-enzyme composition for the conversion of lignocellulosic material to fermentable sugars). Genetic modification of a microorganism can be accomplished using classical strain development and/or molecular genetic techniques. Such techniques known in the art and are generally disclosed for microorganisms, for example, in Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Labs Press or Molecular Cloning: A Laboratory Manual, third edition (Sambrook and Russel, 2001), (jointly referred to herein as “Sambrook”). The references of Sambrook, ibid., are incorporated by reference herein in its entirety. A genetically modified microorganism can include a microorganism in which nucleic acid molecules have been inserted, deleted or modified (i.e., mutated; e.g., by insertion, deletion, substitution, and/or inversion of nucleotides), in such a manner that such modifications provide the desired effect within the microorganism.

In one embodiment, a genetically modified microorganism can endogenously contain and express an enzyme or a multi-enzyme composition for the conversion of lignocellulosic material to fermentable sugars, and the genetic modification can be a genetic modification of one or more of such endogenous enzymes, whereby the modification has some effect on the ability of the microorganism to convert lignocellulosic material to fermentable sugars (e.g., increased expression of the protein by introduction of promoters or other expression control sequences, or modification of the coding region by homologous recombination to increase the activity of the encoded protein).

In another embodiment, a genetically modified microorganism can endogenously contain and express an enzyme for the conversion of lignocellulosic material to fermentable sugars, and the genetic modification can be an introduction of at least one exogenous nucleic acid sequence (e.g., a recombinant nucleic acid molecule), wherein the exogenous nucleic acid sequence encodes at least one additional enzyme useful for the conversion of lignocellulosic material to fermentable sugars and/or a protein that improves the efficiency of the enzyme for the conversion of lignocellulosic material to fermentable sugars. In this aspect of the invention, the microorganism can also have at least one modification to a gene or genes comprising its endogenous enzyme(s) for the conversion of lignocellulosic material to fermentable sugars.

In yet another embodiment, the genetically modified microorganism does not necessarily endogenously (naturally) contain an enzyme for the conversion of lignocellulosic material to fermentable sugars, but is genetically modified to introduce at least one recombinant nucleic acid molecule encoding at least one enzyme or a multiplicity of enzymes for the conversion of lignocellulosic material to fermentable sugars. Such a microorganism can be used in a method of the invention, or as a production microorganism for crude fermentation products, partially purified recombinant enzymes, and/or purified recombinant enzymes, any of which can then be used in a method of the present invention.

Once the proteins (enzymes) are expressed in a host cell, a cell extract that contains the activity to test can be generated. For example, a lysate from the host cell is produced, and the supernatant containing the activity is harvested and/or the activity can be isolated from the lysate. In the case of cells that secrete enzymes into the culture medium, the culture medium containing them can be harvested, and/or the activity can be purified from the culture medium. The extracts/activities prepared in this way can be tested using assays known in the art. Accordingly, methods to identify multi-enzyme compositions capable of degrading lignocellulosic biomass are provided.

Artificial substrates, or complex mixtures of polymeric carbohydrates and lignin, or actual lignocellulose can be used in such tests. One assay that may be used to measure the release of sugars and oligosaccharides from these complex substrates is the dinitrosalicylic acid assay (DNS). In this assay, the lignocellulosic material such as DDG is incubated with enzymes(s) for various times and reducing sugars are Measured.

The invention also contemplates genetically modified plants transformed with one or more nucleic acid molecules of the invention. The plants may be used for production of the enzymes, and/or as the lignocellulosic material used as a substrate in the methods of the invention. Methods to generate recombinant plants are known in the art. For instance, numerous methods for plant transformation have been developed, including biological and physical transformation protocols. See, for example. Miki et al., “Procedures for Introducing Foreign DNA into Plants” in Methods in Plant Molecular Biology and Biotechnology, Glick, B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton, 1993) pp. 67-88. In addition, vectors and in vitro culture methods for plant cell or tissue transformation and regeneration of plants are available. See, for example, Gruber et al., “Vectors for Plant Transformation” in Methods in Plant Molecular Biology and Biotechnology, Glick, B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton, 1993) pp. 89-119.

The most widely utilized method for introducing an expression vector into plants is based on the natural transformation system of Agrobacterium. See, for example. Horsch et al., Science 227:1229 (1985). A. tumefaciens and A. rhizogenes are plant pathogenic soil bacteria which genetically transform plant cells. The Ti and Ri plasmids of A. tumefaciens and A. rhizogenes, respectively, carry genes responsible for genetic transformation of the plant. See, for example. Kado, C. I., Crit. Rev. Plant. Sci. 10:1 (1991). Descriptions of Agrobacterium vector systems and methods for Agrobacterium-mediated gene transfer are provided by numerous references, including Gruber et al. supra, Miki et al., supra, Moloney et al., Plant Cell Reports 8:238 (1989), and U.S. Pat. Nos. 4,940,838 and 5,464.763.

Another generally applicable method of plant transformation is microprojectile-mediated transformation wherein DNA is carried on the surface of microprojectiles. The expression vector is introduced into plant tissues with a biolistic device that accelerates the microprojectiles to speeds sufficient to penetrate plant cell walls and membranes. Sanford et al. Part. Sci. Technol. 5:27 (1987), Sanford, J. C., Trends Biotech. 6:299 (1988), Sanford, J. C., Physiol. Plant 79:206 (1990), Klein et al., Biotechnology 10:268 (1992).

Another method for physical delivery of DNA to plants is sonication of target cells. Zhang et al., Bio/Technology 9:996 (1994 Alternatively, liposome or spheroplast fusion have been used to introduce expression vectors into plants. Deshayes et al., EMBO J., 4:2731 (1985), Christou et al., Proc Natl. Acad. Sci. USA 84:3962 (1987). Direct uptake of DNA into protoplasts using CaCl₂ precipitation, polyvinyl alcohol or poly-L-ornithine have also been reported. Hain et al., Mol. Gen. Genet. 199:161 (1985) and Draper et al., Plant Cell Physiol. 23:451 (1982). Electroporation of protoplasts and whole cells and tissues have also been described. Donn et al., In Abstracts of VIIth International Congress on Plant Cell and Tissue Culture IAPTC. A2-38, p. 53 (1990); D'Halluin et al., Plant Cell 4:1495-1.505 (1992) and Spencer et al. Plant Mol. Biol. 24:51-61 (1994).

Another embodiment of the present invention relates to an isolated binding agent capable of selectively binding to a protein of the present invention. Suitable binding agents may be selected from an antibody, an antigen binding fragment, or a binding partner. The binding agent selectively binds to an amino acid sequence selected from SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11, SEQ ID NO:14, SEQ ID NO:17, SEQ NO:20, SEQ ID NO:23, SEQ ID NO:26, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38, SEQ ID NO:41, SEQ ID NO:44, SEQ ID NO:47, SEQ ID NO:50, SEQ ID NO:53. SEQ ID NO:56, SEQ ID NO:59, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77, SEQ ID NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, SEQ ID NO:92, or SEQ ID NO:94, including to any fragment of any of the above sequences comprising at least one antibody binding epitope.

According to the present invention, the phrase “selectively binds to” refers to the ability of an antibody, antigen binding fragment or binding partner of the present invention to preferentially bind to specified proteins. More specifically, the phrase “selectively binds” refers to the specific binding of one protein to another (e.g., an antibody, fragment thereof, or binding partner to an antigen), wherein the level of binding, as measured by any standard assay (e.g., an immunoassay), is statistically significantly higher than the background control for the assay. For example, when performing an immunoassay, controls typically include a reaction well/tube that contain antibody or antigen binding fragment alone (i.e., in the absence of antigen), wherein an amount of reactivity (e.g., non-specific binding to the well) by the antibody or antigen binding fragment thereof in the absence of the antigen is considered to be background. Binding can be measured using a variety of methods standard in the art including enzyme immunoassays (e.g., ELISA), immunoblot assays, etc.).

Antibodies are characterized in that they comprise immunoglobulin domains and as such, they are members of the immunoglobulin superfamily of proteins. An antibody of the invention includes polyclonal and monoclonal antibodies, divalent and monovalent antibodies, bi- or multi-specific antibodies, serum containing such antibodies, antibodies that have been purified to varying degrees, and any functional equivalents of whole antibodies. Isolated antibodies of the present invention can include serum containing such antibodies, or antibodies that have been purified to varying degrees. Whole antibodies of the present invention can be polyclonal or monoclonal. Alternatively, functional equivalents of whole antibodies, such as antigen binding fragments in which one or more antibody domains are truncated or absent (e.g., Fv, Fab, Fab′, or F(ab)₂ fragments), as well as genetically-engineered antibodies or antigen binding fragments thereof, including single chain antibodies or antibodies that can bind to more than one epitope (e.g., bi-specific antibodies), or antibodies that can bind to one or more different antigens (e.g., bi- or multi-specific antibodies), may also be employed in the invention. Methods for the generation and production of antibodies are well known in the art.

Monoclonal antibodies may be produced according to the methodology of Kohler and Milstein (Nature 256:495-497, 1975). Non-antibody polypeptides, sometimes referred to as binding partners, are designed to bind specifically to a protein of the invention. Examples of the design of such polypeptides, which possess a prescribed ligand specificity are given in Beste et al. (Proc. Natl. Acad. Sci. 96:1898-1903, 1999), incorporated herein by reference in its entirety. In one embodiment, a binding agent of the invention is immobilized on a substrate such as: artificial membranes, organic supports, biopolymer supports and inorganic supports such as for use in a screening assay.

Proteins of the present invention, at least one protein of the present invention, compositions comprising such protein(s) of the present invention, and multi-enzyme compositions (examples of which are described above) may be used in any method where it is desirable to hydrolyze glycosidic linkages in lignocellulosic material, or any other method wherein enzymes of the same or similar function are useful.

In one embodiment, the present invention includes the use of at least one protein of the present invention, compositions comprising at least one protein of the present invention, or multi-enzyme compositions in methods for hydrolyzing lignocellulose and the generation of fermentable sugars therefrom. In one embodiment, the method comprises contacting the lignocellulosic material with an effective amount of one or more proteins of the present invention, composition comprising at least one protein of the present invention, or a multi-enzyme composition, whereby at least one fermentable sugar is produced (liberated). The lignocellulosic material may be partially or completely degraded to fermentable sugars. Economical levels of degradation at commercially viable costs are contemplated.

Typically, the amount of enzyme or enzyme composition contacted with the lignocellulose will depend upon the amount of glucan present in the lignocellulose. In some embodiments, the amount of enzyme or enzyme composition contacted with the lignocellulose may be from about 0.1 to about 200 mg enzyme or enzyme composition per gram of glucan; in other embodiments, from about 3 to about 20 mg enzyme or enzyme composition per gram of glucan. The invention encompasses the use of any suitable or sufficient amount of enzyme or enzyme composition between about 0.1 mg and about 200 mg enzyme per gram glucan, in increments of 0.05 mg (i.e., 0.1 mg, 0.15 mg, 0.2 mg . . . 199.9 mg, 199.95 mg, 200 mg).

In a further embodiment, the invention provides a method for degrading DDG, preferably, but not limited to, DDG derived from corn, to sugars. The method comprises contacting the DDG with a protein of the present invention, a composition comprising at least one protein of the present invention, or a multi-enzyme composition. In certain embodiments, at least 10% of fermentable sugars are liberated. In other embodiment, the at least 15% of the sugars are liberated, or at least 20% of the sugars are liberated, or at least 23% of the sugars are liberated, or at least 24% of the sugars are liberated, or at least 25% of the sugars are liberated, or at least 26% of the sugars are liberated, or at least 27% of the sugars are liberated, or at least 28% of the sugars are liberated.

In another embodiment, the invention provides a method for producing fermentable sugars comprising cultivating a genetically modified microorganism of the present invention in a nutrient medium comprising a lignocellulosic material, whereby fermentable sugars are produced.

Also provided are methods that comprise further contacting the lignocellulosic material with at least one accessory enzyme. Accessory enzymes have been described elsewhere herein. The accessory enzyme or enzymes may be added at the same time, prior to, or following the addition of a protein of the present invention, a composition comprising at least one protein of the present invention, or a multi-enzyme composition, or can be expressed (endogenously or overexpressed) in a genetically modified microorganism used in a method of the invention. When added simultaneously, the protein of the present invention, a composition comprising at least one protein of the present invention, or a multi-enzyme composition will be compatible with the accessory enzymes selected. When the enzymes are added following the treatment with the protein of the present invention, a composition comprising at least one protein of the present invention, or a multi-enzyme composition, the conditions (such as temperature and pH) may be altered to those optimal for the accessory enzyme before, during, or after addition of the accessory enzyme. Multiple rounds enzyme addition are also encompassed. The accessory enzyme may also be present in the lignocellulosic material itself as a result of genetically modifying the plant. The nutrient medium used in a fermentation can also comprise one or more accessory enzymes.

In some embodiments, the method comprises a pretreatment process. In general, a pretreatment process will result in components of the lignoncellulose being more accessible for downstream applications or so that it is more digestible by enzymes following treatment in the absence of hydrolysis. The pretreatment can be a chemical, physical or biological pretreatment. The lignocellulose may have been previously treated to release some or all of the sugars, as in the case of DDG. Physical treatments, such as grinding, boiling, freezing, milling, vacuum infiltration, and the like may also be used with the methods of the invention.

In one embodiment, the heat treatment comprises heating the lignocellulosic material to 121° C. for 15 minutes. A physical treatment such as milling can allow a higher concentration of lignocellulose to be used in the methods of the invention. A higher concentration refers to about 20%, up to about 25%, up to about 30%, up to about 35%, up to about 40%, up to about 45%, or up to about 50% lignocellulose. The lignocellulose may also be contacted with a metal ion, ultraviolet light, ozone, and the like. Additional pretreatment processes are known to those skilled in the art, and can include, for example, organosolv treatment, steam explosion treatment, lime impregnation with steam explosion treatment, hydrogen peroxide treatment, hydrogen peroxide/ozone (peroxone) treatment, acid treatment, dilute acid treatment, and base treatment, including ammonia fiber explosion (AFEX) technology. Details on pretreatment technologies and processes can be found in Wyman et al., Bioresource Tech. 96:1959 (2005); Wyman et al., Bioresource Tech. 96:2026 (2005); Hsu, “Pretreatment of biomass” In Handbook on Bioethanol: Production and Utilization, Wyman, Taylor and Francis Eds., p. 179-212 (1996); and Mosier et al., Bioresource Tech. 96:673 (2005).

In an additional embodiment, the method comprises detoxifying the lignocellulosic material. Dextoxification may be desirable in the event that inhibitors are present in the lignocellulosic material. Such inhibitors can be generated by a pretreatment process, deriving from sugar degradation or are direct released from the lignocellulose polymer. Detoxifying can include the reduction of their formation by adjusting sugar extraction conditions; the use of inhibitor-tolerant or inhibitor-degrading strains of microorganisms. Detoxifying can also be accomplished by the addition of ion exchange resins, active charcoal, enzymatic detoxification using, e.g., laccase, and the like. In some embodiments, the proteins, compositions or products of the present invention further comprises detoxifying agents.

In some embodiments, the methods may be performed one or more times in whole or in part. That is, one may perform one or more pretreatments, followed by one or more reactions with a protein of the present invention, composition or product of the present invention and/or accessory enzyme. The enzymes may be added in a single dose, or may be added in a series of small doses. Further, the entire process may be repeated one or more times as necessary. Therefore, one or more additional treatments with heat and enzymes are contemplated.

The methods described above result in the production of fermentable sugars. During, or subsequent to the methods described, the fermentable sugars may be recovered. In the case of a cultivation of microorganisms, the sugars can be recovered through a continuous, batch or fed-batch method. The sugars recovered can be concentrated or purified. Recovery may occur by any method known in the art, including, but not limited to, washing, gravity flow, pressure, chromatography, extraction, crystallization (e.g., evaporative crystallization), membrane separation, reverse osmosis, distillation, and filtration. The sugars can be subjected further processing; e.g., they can also be sterilized, for example, by filtration.

In a related embodiment, the invention provides means for improving quality of lignocellulosic material, including DDG for animal nutrition. In one embodiment, the treated lignocellulosic material (e.g., a lignocellulosic material which has been saccharified) is recovered (e.g., has the soluble sugars removed). The recovered material can be used as an animal feed additive. It is believed that the recovered material will have beneficial properties for animal nutrition, possibly due to a higher protein content. In some embodiments, the amount of enzyme or enzyme composition contacted with the lignocellulosic material may be from about 0.0001% to about 1.0% of the weight of the lignocellulosic material; in other embodiments, from about 0.005% to about 0.1% of the weight of the lignocellulosic material. The invention includes the use of any amount of enzyme or enzyme composition between about 0.0001% and about 1.0%, in increments of 0.0001 (i.e. 0.0001, 0.0002, 0.0003 . . . etc.).

In an additional embodiment, the invention provides a method for producing an organic substance, comprising saccharifying a lignocellulosic material with an effective amount of a protein of the present invention or a composition comprising at least one protein of the present invention, fermenting the saccharified lignocellulosic material obtained with one or more fermentating microorganisms, and recovering the organic substance from the fermentation. Sugars released from biomass can be converted to useful fermentation products including but not limited to amino acids, vitamins, pharmaceuticals, animal feed supplements, specialty chemicals, chemical feedstocks, plastics, solvents, fuels, or other organic polymers, lactic acid, and ethanol, including fuel ethanol. Specific products that may be produced by the methods of the invention include, but not limited to, biofuels (including ethanol); lactic acid; plastics; specialty chemicals; organic acids, including citric acid, succinic acid and maleic acid; solvents; animal feed supplements; pharmaceuticals; vitamins; amino acids, such as lysine, methionine, tryptophan, threonine, and aspartic acid; industrial enzymes, such as proteases, cellulases, amylases, glucanases, lactases, lipases, lyases, oxidoreductases, and transferases; and chemical feedstocks. The methods of the invention are also useful to generate feedstocks for fermentation by fermenting microorganisms. In one embodiment, the method further comprises the addition of at least one fermenting organism. As used herein, “fermenting organism” refers to an organism capable of fermentation, such as bacteria and fungi, including yeast. Such feedstocks have additional nutritive value above the nutritive value provided by the liberated sugars.

Proteins of the present invention and compositions comprising at least one protein of the present invention are also useful in a variety of other applications involving the hydrolysis of glycosidic linkages in lignocellulosic material, such as stone washing, color brightening, depilling and fabric softening, as well as other applications well known in the art. Proteins of the present invention and compositions comprising at least one protein of the present invention are also readily amenable to use as additives in detergent and other media used for such applications. These and other methods of use will readily suggest themselves to those of skill in the art based on the invention described herein.

In one embodiment of this invention, proteins and compositions of the present invention can be used in stone washing procedures for fabrics or other textiles. In some embodiments, the proteins and compositions can be used in stone washing procedures for denim jeans. By way of example, the method for stone washing the fabric comprises contacting the fabric with a protein or composition of the present invention. In an additional embodiment, the protein or composition of the present invention is included in a detergent composition, as described below. A preferred pH range of stone wash applications is between about 5.5 to 7.5, most preferably at about pH 6 to about 7. One of skill in the art will know how to regulate the amount or concentration of the protein or composition produced by this invention based on such factors as the activity of the enzyme and the wash conditions, including but not limited to temperature and pH. Examples of these uses can be found in U.S. Patent Application Publication No. 2003/0157595, the contents of which are hereby incorporated by reference.

In yet another embodiment of this invention, the cellulose compositions of this invention can be used to reduce or eliminate the harshness associated with a fabric or textile by contacting the fabric or textile with a protein or composition of the present invention. In some embodiments, the fabric or textile may be made from cellulose or cotton. By way of example, a preferred range for reducing or eliminating the harshness associated with a fabric or textile is between about pH 8 to about 12, or between about pH 10 to about 11.

The proteins or compositions of the subject invention can be used in detergent compositions. In one embodiment, the detergent composition may comprise at least one protein or composition of the present invention and one or more surfactants. The detergent compositions may also include any additional detergent ingredient known in the art. Detergent ingredients contemplated for use with the detergent compositions of the subject invention include, but are not limited to, detergents, buffers, surfactants, bleaching agents, softeners, solvents, solid forming agents, abrasives, alkalis, inorganic electrolytes, cellulose activators, antioxidants, builders, silicates, preservatives, and stabilizers. The detergent compositions of this invention preferably employ a surface active agent, i.e., surfactant, including anionic, non-ionic, and ampholytic surfactants well known for their use in detergent compositions. In addition to the at least one protein or composition of the present invention and the surface active agent, the detergent compositions of this invention can additionally contain one or more of the following components: the enzymes amylases, cellulases, proteinase, lipases, oxido-reductases, peroxidases and other enzymes; cationic surfactants and long-chain fatty acids; builders; antiredeposition agents; bleaching agents; bluing agents and fluorescent dyes; caking inhibitors; masking agents for factors inhibiting the cellulase activity; cellulase activators; antioxidants; and solubilizers. In addition, perfumes, preservatives, dyes, and the like can be used, if desired, with the detergent compositions of this invention. Examples of detergent compositions employing cellulases are exemplified in U.S. Pat. Nos. 4,435,307; 4,443,355; 4,6611,289; 4,479,881; 5,120,463, each of which is incorporated herein by reference in its entirety for all purposes.

When a detergent base used in the present invention is in the form of a powder, it may be one which is prepared by any known preparation method including a spray-drying method and/or a granulation method. The granulation method are the most preferred because of the non-dusting nature of granules compared to spray thy products. The detergent base obtained by the spray-drying method is hollow granules which are obtained by spraying an aqueous slurry of heat-resistant ingredients, such as surface active agents and builders, into a hot space. The granules have a size of from about 50 to about 2000 micrometers. After the spray-drying, perfumes, enzymes, bleaching agents, and/or inorganic alkaline builders may be added. With a highly dense, granular detergent base obtained by such as the spray-drying-granulation method, various ingredients may also be added after the preparation of the base. When the detergent base is a liquid, it may be either a homogenous solution or an inhomogeneous solution.

Other textile applications in which proteins and compositions of the present invention may be used include, but are not limited to, garment dyeing applications such as enzymatic mercerizing of viscose, bio-polishing applications, enzymatic surface polishing; biowash (washing or washing down treatment of textile materials), enzymatic microfibrillation, enzymatic “cottonization” of linen, ramie and hemp; and treatment of Lyocel or Newcell (i.e., “TENCEL” from Courtauld's), Cupro and other cellulosic fibers or garments, dye removal from dyed cellulosic substrates such as dyed cotton (Leisola & Linko—(1976) Analytical Biochemistry, v. 70, p. 592. Determination Of The Solubilizing Activity Of A Cellulase Complex With Dyed Substrates; Blum & Stahl—Enzymic Degradation Of Cellulose Fibers; Reports of the Shizuoka Prefectural Hamamatsu Textile Industrial Research Institute No. 24 (1985)), as a bleaching agent to make new indigo dyed denim look old (Fujikawa—Japanese Patent Application Kokai No. 50-132269), to enhance the bleaching action of bleaching agents (Suzuki—Great Britain Patent No. 2 094 826), and in a process for compositions for enzymatic desizing and bleaching of textiles (Windbichtler et al., U.S. Pat. No. 2,974,001. Another example of enzymatic desizing using cellulases is provided in Bhatawadekar (May 1983) Journal of the Textile Association, pages 83-86.

The amount of enzyme or enzyme composition contacted with a textile may vary with the particular application. Typically, for biofinishing and denim washing applications, from about 0.02 wt. % to about 5 wt. % of an enzyme or enzyme composition may be contacted with the textile. In some embodiments, from about 0.5 wt. % to about 2 wt. % of an enzyme or enzyme composition may be contacted with the textile. For bioscouring, from about 0.1 to about 10, or from about 0.1 to about 1.0 grams of an enzyme or enzyme composition per kilogram of textile may be used, including any amount between about 0.1 grams and about 10 grams, in increments of 0.1 grams.

In other embodiments, the proteins or compositions of the present invention can be used in the saccharification of lignocellulose biomass from agriculture, forest products, municipal solid waste, and other sources, for biobleaching of wood pulp, and for de-inking of recycled print paper all by methods known to one skilled in the art.

The amount of enzyme or enzyme composition used for pulp and paper modification (e.g., biobleaching of wood pulp, de-inking of paper, or biorefining of pulp for paper making) typically varies depending upon the stock that is used, the pH and temperature of the system, and the retention time. In certain embodiments, the amount of enzyme or enzyme composition contacted with the paper or pulp may be from about 0.01 to about 50 U; from about 0.1 to about 15 U; or from about 0.1 to about 5 U of enzyme or enzyme composition per dry gram of fiber, including any amount between about 0.01 and about 50 U, in 0.01 U increments. In other embodiments, the amount of enzyme or enzyme composition contacted with the paper or pulp may be from about 1 to about 2000 grams or from about 100 to about 500 grams enzyme or enzyme composition per dry ton of pulp, including any amount between about 1 and about 2000 grams, in 1 gram increments.

Proteins or compositions of the present invention can added to wastewater to reduce the amount of solids such as sludge or to increase total biochemical oxygen demand (BOD) and chemical oxygen demand (COD) removal. For example, proteins or compositions of the present invention can be used to transform particulate COD to soluble COD in wastewater produced from grain/fruit/cellulose industrial processes or to increase the BOD/COD ratio by increasing waste biodegradability (soluble lower molecular weight polymers in cellulosic/hemicellulosic wastes are typically more readily biodegradable than non-soluble material). In biological wastewater treatment systems, proteins or compositions of the present invention can also be used to increase waste digestion by aerobic and/or anaerobic bacteria.

Chitinases of the present invention (e.g., SEQ ID NOS: 56 and 59) can hydrolyze the β-1,4-glycosidic linkage present in chitin and thus may be used to degrade chitin-containing materials. Examples of chitin-containing materials include fungal cell walls, insect exoskeletons, the eggs of parasitic worms, and crustacean shells.

Chitinases may be used to inhibit or reduce fungal growth, including the treatment of fungal infections such as those caused by nail fungi. For example, chitinases of the present invention may be applied to any fungus or area susceptible to fungal growth. Chitinases may also be used to coat or treat seeds and flower bulbs to prevent the growth of fungi. Further, chitinases may be added to fungal cultures to lower culture viscosity by increasing cell wall degradation. Chitinases may also by used as lysing enzymes for the generation of protoplasts from fungi (see, e.g., Yano et al., Biosci Biotechnol Biochem. 70:1754 (2006).

Chitinases or compositions containing chitinases may be used as a biological control agent such as an insecticide (see, e.g., Kramer et al., Insect Biochem Mol. Biol. 27:887 (1997). Chitinases of the present invention have been shown to be effective for Controlling white-fly larvae in laboratory tests. Thus, chitinases may be applied to crops, plants and the like to control insect infestations.

Chitin has also been suggested to play a role in inducing allergic inflammation and asthma (see Reese et al., Nature 447:92 (2007)). Accordingly, chitinases of the present invention may be administered to a subject to reduce allergic inflammatory responses induced by chitin or to reduce the symptoms of asthma.

Exemplary methods according to the invention are presented below. Examples of the methods described above may also be found in the following references, all of which are incorporated herein in their entirties: Trichoderma & Gliocladium. Volume 2. Enzymes, biological control and commercial applications. Editors: Gary E. Hannan, Christian P. Kubicek. Taylor & Francis Ltd 1998, 393 (in particular, chapters 14, 15 and 16) Helmut Uhlig. Industrial enzymes and their applications. Translated and updated by Elfriede M. Linsmaier-Bednar. John Wiley & Sons, Inc 1998, p. 454 (in particular, chapters 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.9, 5.10, 5.11, and 5.13) For saccharification applications: Hahn-Hägerdal, B., Galbe, M., Gorwa-Grauslund, M. F. Lidén, Zacchi, G. Bio-ethanol—the fuel of tomorrow from the residues of today. Trends in Biotechnology. 2006, 24 (12), 549-556; Mielenz, J. R. Ethanol production from biomass: technology and commercialization status. Current Opinion in Microbiology. 2001, 4, 324-329; Himmel. M. E., Ruth, M. F. Wyman, C. E. Cellulase for commodity products from cellulosic biomass. Current Opinion in Biotechnology. 1999, 10, 358-364; Sheehan, J. Himmel, M. Enzymes, energy, and the environment: a strategic perspective on the U.S. Department of Energy's Research and Development Activities for Bioethanol. Biotechnology Progress. 1999, 15, 817-827. For textile processing applications: Galante, Y. M., Formantici, C. Enzyme applications in detergency and in manufacturing industries. Current Organic Chemistry. 2003, 7, 1399-1422. For pulp and paper applications: Bajpai, P., Bajpai, P. K Deinking with enzymes: a review. TAPPI Journal. 1998, 81(12), 111-117; Viikari, L., Pere, J., Suurnäkki, A., Oksanen, T., Buchert, J. Use of cellulases in pulp and paper applications. In: “Carbohydrates from Trichoderma reesei and other microorganisms. Structure, Biochemistry, Genetics and Applications.” Editors: Mark Claessens, Wim Nerinckx, and Kathleen Piens. The Royal Society of Chemistry 1998, 245-254. For food and beverage applications: Roller, S. Dea, I.C.M. Biotechnology in the production and modification of biopolymers for foods. Critical Reviews in Biotechnology. 1992, 12(3), 261-277.

Each publication or reference cited herein is incorporated herein by reference in its entirety for all purposes.

The following examples are provided for the purpose of illustration and are not intended to limit the scope of the present invention.

EXAMPLES Example 1

The following example illustrates the Somogyi-Nelson assay used to measure beta-glucanase enzymatic activity.

This assay measures the release of reducing sugars (as glucose equivalents) by the action of β-glucanase on a soluble β-glucan. One β-glucanase unit of activity is the amount of enzyme that liberates 1 micromole of reducing sugars, expressed as glucose equivalents, in one minute at 50° C. and pH 5.0.

Reagents

Acetate buffer (0.05 M, pH 5.0) is prepared as follows. 4.1 g of anhydrous sodium acetate or 6.8 g of sodium acetate*3H₂O is dissolved in distilled water so that the final volume of the solution is 1000 mL (Solution A). In a separate flask, 3.0 g (2.86 mL) of glacial acetic acid is mixed with distilled water to make a total volume of 1000 mL (Solution B). The final 0.05 M acetate buffer, pH 5.0, is prepared by mixing Solution A with Solution B until the pH of the resulting solution is equal to 5.0.

β-glucan from barley (medium viscosity, Megazyme, P-BGBM) is used as the assay substrate. The substrate is milled in a mortar before dissolving. 1% w/v stock solution is prepared as follows. 500 mg of β-glucan is mixed with 50 mL of distilled water and agitated on a magnetic stirrer for 1 hour. After that, the suspension is placed into a Bandelin SONOREX TK52 ultrasonic bath for 10 minutes to destroy undissolved particles and then into a boiling water bath until the solution becomes clear. Finally, the solution is stirred on a magnetic stirrer for 30 minutes. The solution is typically stable for 2 days.

The Somogyi reagent is prepared as follows. 24 g of anhydrous sodium carbonate and 12 g of sodium-potassium tartrate tetrahydrate are dissolved in 250 mL of distilled water. A solution of copper sulfate pentahydrate (4 g in 40 mL of distilled water) is added on stirring, and then 16 g of sodium bicarbonate is dissolved to obtain Solution A. In a separate flask, 180 g of sodium sulfate is dissolved in 500 mL of hot (˜80° C.) distilled water and boiled for 5 minutes (Solution B). Solution A is mixed with Solution B and the final volume is adjusted to 1.000 mL. The reagent is stable for 2-3 months on storing in a dark glass vessel.

The Nelson reagent is prepared as follows. 50 g of ammonium molybdate is dissolved in 900 mL of hot (˜60° C.) distilled water. The solution is cooled to 5-10° C. and 42 g of concentrated sulfuric acid containing 6 g of sodium arsenate are carefully added on stirring. The volume of the mixture is adjusted to 1000 mL. The flask is incubated at 40° C. for 48 hours and then the solution is filtered if necessary. The reagent is stable for 2-3 months.

Using the above reagents, the assay is performed as detailed below.

Reagent Blank

0.5 mL of 0.05 M sodium acetate buffer is mixed in a graduated glass test tube (1.5 cm×15 cm) with 0.5 mL of Somogyi reagent and incubated in a boiling water bath for 40 minutes. Then, the test tube is cooled in an ice or cold water bath and 0.5 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 5 mL with distilled water.

Enzyme Sample

0.25 mL of 1% w/v β-glucan stock solution is mixed with 0.15 mL of 0.05 M acetate buffer, pH 5.0, in graduated glass test tubes (1.5 cm×15 cm) and preheated at 50° C. for 5 minutes. Enzyme sample is suitably diluted by the 0.05 M sodium acetate buffer (the dilution of the enzyme sample is chosen so that A₆₁₀ should be between 0.05 and 0.4 units of optical density). 0.1 mL of suitably diluted enzyme sample is added to 0.4 mL of the preheated substrate solution, mixed and incubated at 50° C. for 10 minutes. After exactly 10 minutes of incubation, 0.5 mL of Somogyi reagent is added, and test tubes are placed into a boiling water bath for 40 minutes. Then, the test tubes are cooled in an ice or cold water bath and 0.5 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 5 mL with distilled water. Then, the absorbance at 610 nm (A₆₁₀) is measured against the reagent blank as A₅ (enzyme sample).

Enzyme Blank

0.4 mL of 0.05 M sodium acetate buffer is mixed in a graduated glass test tube (1.5 cm×15 cm) with 0.1 mL of enzyme sample having the same dilution as above. 0.5 mL of Somogyi reagent is added and the test tube is incubated in a boiling water bath for 40 minutes. Then, the test tube is cooled in an ice or cold water bath and 0.5 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 5 mL with distilled water. Then, the absorbance at 610 nm (A₆₁₀) is measured against the reagent blank as A_(EB) (enzyme blank).

Substrate Blank

0.25 mL of 1% w/v β-glucan stock solution is mixed with 0.25 mL of 0.05 M acetate buffer, pH 5.0, in a graduated glass test tube (1.5 cm×15 cm), 0.5 mL of Somogyi reagent is added, and the test tube is placed into a boiling water bath for 40 minutes. Then, the test tube is cooled in an ice or cold water bath and 0.5 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 5 mL with distilled water. Then, the absorbance at 610 nm (A₆₁₀) is measured against the reagent blank as A_(SB) (substrate blank). The value of A_(SB) should not exceed 0.05 units of optical density.

All enzyme samples and enzyme and substrate blanks should be boiled together.

Standard Calibration Plot

Stock glucose solution (1 mg/mL) is prepared by dissolving 100 mg of D-glucose in 100 mL of 0.05 M acetate buffer, pH 5.0. Then, different dilutions of stock glucose solution are prepared as follows:

0.05M acetate Stock solution (mL) buffer (mL) Glucose concentration (mg/mL) 0.05 4.95 0.01 0.10 4.90 0.02 0.15 4.85 0.03 0.20 4.80 0.04 0.25 4.75 0.05 0.30 4.70 0.06 0.35 4.65 0.07 0.40 4.60 0.08 0.45 4.55 0.09 0.50 4.50 0.10

Samples (0.5 mL) of glucose solution with different dilutions are placed to graduated glass test tubes (1.5 cm×1.5 cm). 0.5 mL of Somogyi reagent is added and test tubes are placed into a boiling water bath for 40 minutes. Then, the test tubes are cooled in an ice or cold water bath and 0.5 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 5 mL with distilled water. Then, the absorbance at 610 nm (A₆₁₀) is measured against the reagent blank. The following typical A₆₁₀ data obtained with different glucose dilutions are given below:

Glucose, mg/mL 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10 A₆₁₀ 0.11 0.20 0.28 0.41 0.48 0.60 0.72 0.79 0.93 1.06 Absorbance (A₆₁₀) on the y-axis versus glucose concentration (G, mg/mL) on the x-axis is plotted to generate a standard calibration plot such as that shown in the FIG. 11. From FIG. 11, the inverse of the slop (l/a=0.098) is calculated.

Calculation of Activity

Activity is calculated as follows: activity (IU/mL)=1/a*ΔA₆₁₀*DF*2.78, where 1/a—inverse of the slope calculated from the standard calibration plot, ΔA₆₁₀=A_(S) (enzyme sample)−A_(EB) (enzyme blank)−A_(SB) (substrate blank), DF is the enzyme dilution factor, and 2.78 is the coefficient that accounts for additional 5-fold enzyme dilution in the reaction mixture (0.1 mL enzyme+0.4 mL substrate), reaction time (10 minutes) and molecular weight of glucose (0.18016 mg/micromole), i.e. 5/(10*0.18016)=2.78

An example calculation is supplied below.

B4 UF concentrate DF ΔA₆₁₀ 20,000 0.545 40,000 0.316 80,000 0.154 β-glucanase activity (IU/mL)=0.098*0.316*40000*2.78=3444

Example 2

The following example illustrates the assays used to measure beta-glucosidase, α-galactosidase and β-galactosidase enzymatic activities.

This assay measures the release of p-nitrophenol by the action of β-glucosidase on p-nitrophenyl β-D-glucopyranoside (PNPG). Modifications to the assay for measuring α-galactosidase and β-galactosidase enzymatic activities are discussed below. One β-glucosidase unit of activity is the amount of enzyme that liberates 1 micromole of p-nitrophenol in one minute at 40° C. and pH 5.0.

Reagents

Acetate buffer (0.1 M, pH 5.0) is prepared as follows. 8.2 g of anhydrous sodium acetate or 13.6 g of sodium acetate*3H₂O is dissolved in distilled water so that the final volume of the solution to be 1000 mL (Solution A). In a separate flask, 6.0 g (5.72 mL) of glacial acetic acid is mixed with distilled water to make the total volume of 1000 mL (Solution B). The final 0.1 M acetate buffer, pH 5.0, is prepared by mixing Solution A with Solution B until the pH of the resulting solution is equal to 5.0. PNPG from Sigma (USA) is used as the assay substrate. 6 mg of PNPG is dissolved in 2 mL of distilled water using magnetic stirrer to obtain 10 mM stock solution. The solution is stable for 2 days on storage at 4° C.

The stop reagent (1 M sodium carbonate solution) is prepared as follows. 10.6 g of anhydrous sodium carbonate is dissolved in 80 mL of distilled water, and the solution volume is adjusted to 100 mL. This reagent is used to terminate the enzymatic reaction.

Using the above reagents, the assay is performed as detailed below.

Enzyme Sample

0.09 mL of 10 mM PNPG stock solution is mixed with 0.81 mL of 0.1 M acetate buffer, pH 5.0, and preheated at 40° C. for 5 minutes. The enzyme sample is suitably diluted with the 0.1 M sodium acetate buffer (the dilution of the enzyme sample is chosen so that A₄₀₀ should be between 0.05 and 0.35 units of optical density). 0.1 mL of suitably diluted enzyme sample is added to 0.9 mL of the preheated substrate solution, mixed and incubated at 40° C. for 10 minutes. After exactly 10 minutes of incubation, 0.5 mL of 1 M sodium carbonate solution is added and then the absorbance at 400 nm (A₄₀₀) is measured as A_(S) (enzyme sample).

Substrate Blank

0.09 mL of 10 mM PNPG stock solution is mixed with 0.91 mL of 0.1 M acetate buffer, pH 5.0. Then, 0.5 mL of 1 M sodium carbonate solution is added and the absorbance at 400 nm (A₄₀₀) is measured as A_(SB) (substrate blank).

Calculation of Activity

Activity is calculated as follows: activity (IU/mL)=ΔA₄₀₀*DF*0.082, where ΔA₄₀₀=A_(S) (enzyme sample)−A_(SB) (substrate blank), DF is the enzyme dilution factor, and 0.082 is the coefficient obtained as follows:

$0.082 = \frac{10^{6}}{18300*10*\left( {0.1\text{/}0.0015} \right)}$

where 10⁶ is factor used to convert moles/L in the extinction coefficient to micromoles/L, 18300 M⁻¹ cm⁻¹ is the extinction coefficient of p-nitrophenol released, 10 minutes is the reaction time, and 0.1 mL is the volume of enzyme solution added to 0.0015 L of total assay volume.

An example calculation is supplied below.

B4 UF concentrate DF ΔA₄₀₀ 5,000 0.495 10,000 0.268 20,000 0.144 For DF=10,000: β-glucosidase activity (IU/mL)=0.268*10000*0.082=220 For DF=20,000: β-glucosidase activity (IU/mL)=0.144*20000*0.082=236 Finally, β-glucosidase activity=228 IU/mL, as a mean value between two measurements.

α- and β-Galactosidase Assays

The assay procedures for α- and β-galactosidases are the same as the β-glucosidase assay described above, except that p-nitrophenyl α-D-galactopyranoside and p-nitrophenyl β-D-galactopyranoside are used as substrates, respectively, instead of p-nitrophenyl β-D-glucopyranoside.

Example 3

The following example illustrates the Somogyi-Nelson assay used to measure CMCase enzymatic activity.

This assay measures the release of reducing sugars (as glucose equivalents) by the action of cellulase on a soluble cellulosic substrate (CMC). One CMCase unit of activity is the amount of enzyme that liberates 1 micromole of reducing sugars, expressed as glucose equivalents, in one minute at 50° C., pH 5.0, 0.05 M sodium acetate buffer.

Reagents

Acetate buffer (0.05 M, pH 5.0) is prepared as follows. 4.1 g of anhydrous sodium acetate or 6.8 g of sodium acetate*3H₂O is dissolved in distilled water so that the final volume of the solution to be 1000 mL (Solution A). In a separate flask, 3.0 g (2.86 mL) of glacial acetic acid is mixed with distilled water to make the total volume of 1.000 mL (Solution B). The final 0.05 M acetate buffer, pH 5.0, is prepared by mixing Solution A with Solution B until the pH of the resulting solution is equal to 5.0.

The sodium salt of carboxymethyl cellulose (CMC, medium viscosity, Sigma, C 4888) is used as the substrate. A 1% w/v stock solution is prepared in 0.05 M acetate buffer, pH 5.0, by adding gradually 1.0 g of CMC to 99 mL of the buffer agitated on a magnetic stirrer. The mixture is stirred until the CMC is completely dissolved. The solution is stable for 2 days at 4° C.

The Somogyi reagent is prepared as follows. 24 g of anhydrous sodium carbonate and 12 g of sodium-potassium tartrate tetrahydrate are dissolved in 250 mL of distilled water. The solution of copper sulfate pentahydrate (4 g in 40 mL of distilled water) is added on stirring, and then 16 g of sodium bicarbonate is dissolved to obtain Solution A. In a separate flask, 18.0 g of sodium sulfate is dissolved in 500 mL of hot (˜80° C.) distilled water and boiled for 5 min (Solution B). Solution A is mixed with Solution B and the final volume is adjusted to 1000 mL. The reagent is stable for 2-3 months on storing in a dark glass vessel at room temperature.

The Nelson reagent is prepared as follows. 50 g of ammonium molybdate is dissolved in 900 mL of hot (˜60° C.) distilled water. The solution is cooled to 5-10° C. and 42 g of concentrated sulfuric acid containing 6 g of sodium arsenate are carefully added on stirring. The volume of the mixture is adjusted to 1000 mL. The flask is incubated at 40° C. for 48 hours and then the solution is filtered if necessary. The reagent is stable for 2-3 months at room temperature.

Using the above reagents, the assay is performed as detailed below.

Reagent Blank

0.5 mL of 0.05 M sodium acetate buffer is mixed in a graduated glass test tube (1.5 cm×15 cm) with 0.5 mL of Somogyi reagent and incubated in a boiling water bath for 40 minutes. Then, the test tube is cooled in an ice or cold water bath and 0.5 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 5 mL with distilled water.

Enzyme Sample

0.25 mL of 1% w/v CMC stock solution is preheated in graduated glass test tubes (1.5 cm×15 cm) at 50° C. for 5 minutes. Enzyme sample is suitably diluted by the 0.05 M sodium acetate buffer (the dilution of the enzyme sample is chosen so that A₆₁₀ should be between 0.05 and 0.35 units of optical density) and preheated at 50° C. for 5 minutes. 0.25 mL of suitably diluted enzyme sample is added to 0.25 mL of preheated. CMC stock solution, mixed and incubated at 50° C. for 5 minutes. After exactly 5 minutes of incubation, 0.5 mL of Somogyi reagent is added, and test tubes are placed into a boiling water bath for 40 minutes. Then, the test tubes are cooled in an ice or cold water bath and 0.5 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, 1 mL of acetone is added to dissolve CMC precipitated during the boiling procedure and the solution volume is adjusted to 5 mL with distilled water. Then, the absorbance at 610 nm (A₆₁₀) is measured against the reagent blank as A_(S) (enzyme sample).

Enzyme Blank

0.25 mL of 0.05 M sodium acetate buffer is mixed in a graduated glass test tube (1.5 cm×15 cm) with 0.25 mL of enzyme sample having the same dilution as above. 0.5 mL of Somogyi reagent is added and the test tube is incubated in a boiling water bath for 40 minutes. Then, the test tube is cooled in an ice or cold water bath and 0.5 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 5 mL with distilled water. Then, the absorbance at 610 nm (A₆₁₀) is measured against the reagent blank as A_(B) (enzyme blank).

All enzyme samples and enzyme blanks should be boiled together.

Standard Calibration Plot

A stock glucose solution (1 mg/mL) is prepared by dissolving 100 mg of D-glucose in 100 mL of 0.05 M acetate buffer, pH 5.0. Then, different dilutions of stock glucose solution are prepared as follows:

0.05M acetate Stock solution (mL) buffer (mL) Glucose concentration (mg/mL) 0.05 4.95 0.01 0.10 4.90 0.02 0.15 4.85 0.03 0.20 4.80 0.04 0.25 4.75 0.05 0.30 4.70 0.06 0.35 4.65 0.07 0.40 4.60 0.08 0.45 4.55 0.09 0.50 4.50 0.10

Samples (0.5 mL) of glucose solution with different dilutions are placed to graduated glass test tubes (1.5 cm×15 cm). 0.5 mL of Somogyi reagent is added and test tubes are placed into a boiling water bath for 40 minutes. Then, the test tubes are cooled in an ice or cold water bath and 0.5 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 5 mL with distilled water. Then, the absorbance at 610 nm (A₆₁₀) is measured against the reagent blank. The following typical A₆₁₀ data obtained with different glucose dilutions are given below:

-   -   Glucose, mg/mL 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10     -   A₆₁₀ 0.11 0.20 0.28 0.41 0.48 0.60 0.72 0.79 0.93 1.06         Absorbance (A₆₁₀) on the y-axis versus glucose concentration (G,         mg/mL) on the x-axis is plotted to generate a standard         calibration plot such as that shown in the FIG. 11. From FIG.         11, the inverse of the slop (l/a=0.098) is calculated.

Calculation of Activity

Activity is calculated as follows: CMCase (IU/mL)=1/a*ΔA₆₁₀*DF*2.22, where l/a−inverse of the slope calculated from the standard calibration plot, ΔA₆₁₀=A_(S) (enzyme sample)−A_(B) (enzyme blank). DF—enzyme dilution factor, and 2.22 is the coefficient that accounts for additional 2-fold enzyme dilution in the reaction mixture (0.25 mL enzyme+0.25 mL substrate), reaction time (5 minutes) and molecular weight of glucose (0.18016 mg/micromole), i.e. 2/(5*0.18016)=2.22.

An example calculation is supplied below.

ACE sample DF ΔA₆₁₀ 40,000 0.41 80,000 0.25

CMCase activity (IU/mL)=0.098*0.25*80000*2.22=4351

Example 4

The following example illustrates the Lowry protein assay.

The Lowry procedure is one of the most known and widely used protein assays, being first described in 1951 (Lowry O H, Rosebrough N J, Farr A L. Randall R J (1951) J. Biol. Chem. 193: 265-275). Under alkaline conditions, copper complexes with protein. When Folin's phenol reagent (phospho-molybdic-phosphotungstic reagent) is added, it binds to the protein. Bound reagent is slowly reduced and changes color from yellow to blue.

Stock Solutions and Reagents

Lowry A stock solution is 2% Na₂CO₃ in 0.1 M NaOH. Lowry B stock solution is 1% CuSO₄.5H₂O in distilled water. Lowry C stock solution is 2% sodium potassium tartrate (NaKC₄H₄O₆.4H₂O) in distilled water. Lowry stock reagent is prepared fresh daily by mixing 49 ml Lowry A, 0.5 ml Lowry B and 0.5 ml Lowry C. Commercial Folin's Reagent: Phenol reagent—2N (Folin—Ciocalteau reagent) is diluted 1:1 in distilled water before use and stored in a refrigerator.

Bovine serum albumin (BSA) is used as the assay standard. When BSA is weighed out before use, the protein preparation used to prepare the standard should be salt-free to avoid inaccurate results. BSA is dissolved at a concentration of 1 mg/ml in a buffer similar to the solution for analysis. A series of standard dilutions is prepared where the protein (BSA) concentration is varied in the range of 0.05-0.5 mg/ml.

Assay Procedure

Using the above reagents, the assay is performed as follows. 100 μl of sample is added to each tube followed by 1.0 ml of Lowly stock reagent and the mixture is incubate 10 minutes at room temperature. 100 μl of Folin's reagent is added to each tube and the tubes are further incubated for 40 minutes at room temperature. A absorbance at 750 nm is read on a spectrophotometer against a blank (control) prepared in the same way as the sample except the buffer is added to the tube instead of the analyzed protein. Protein concentration is the determined by reading the absorbance at 750 nm for each sample and plotting the result on a BSA calibration graph prepared from the standard dilutions discussed above.

The Lowry procedure should be carried out with caution since it is subjected to interference by a wide variety of chemicals. Among the chemicals reported to interfere with the Lowry procedure are barbital, CAPS, cesium chloride, citrate, cysteine, diethanolamine, dithiothreitol, EDTA, EGTA, HEPES, mercaptoethanol, Nonidet P-40, phenol, polyvinyl pyrrolidone, sodium deoxycholate, sodium salicylate, thimerosol, Tricine, TRIS and Triton X-100.

Example 5

The following example illustrates the Somogyi-Nelson assay used to measure avicelase activity.

The assay measures the velocity of release of reducing sugars by the action of cellulases on insoluble Avicel cellulose (micro crystalline cellulose) when reducing sugars are assayed by Somogyi-Nelson method as glucose equivalents. One unit of avicelase activity is equal to the amount of enzyme that 1 micromole of reducing sugars, expressed as glucose equivalents (when reducing sugars assayed by Somogyi-Nelson method) in one minute at 40° C., pH 5.0 (0.05 M sodium acetate buffer).

Reagents

Acetate buffer (0.05 M, pH 5.0) is prepared as follows. 4.1 g of anhydrous sodium acetate or 6.8 g of sodium acetate*3H₂O is dissolved in distilled water so that the final volume of the solution to be 1000 mL (Solution A). In a separate flask, 3.0 g (2.86 mL) of glacial acetic acid is mixed with distilled water to make the total volume of 1000 mL (Solution B). The final 0.05 M acetate buffer, pH 5.0, is prepared by mixing Solution A with Solution B until the pH of the resulting solution is equal to 5.0.

Avicel PH 105 (Serva, FRG) (or any other available source of Avicel) is used as the assay substrate. 1% w/v of stock suspension of Avicel is prepared in 0.05 M acetate buffer, pH 5.0, by adding 50 mg of dry Avicel gradually to a vessel with 5 mL of the buffer agitated on a magnetic stirrer. After that the obtained Avicel suspension is mixed on a magnetic stirrer during 1 hour at room temperature (for swelling of Avicel). 1% w/v stock suspension of Avicel can be stored in covered vessel for 5-7 days at 4° C.

The Somogyi reagent is prepared as follows. 24 g of anhydrous sodium carbonate and 12 g of sodium-potassium tartrate*4H₂O are dissolved in 250 mL of distilled water. The solution of copper sulfate*5H₂O (4 g in 40 mL of distilled water) is added on stirring, and then 16 g of sodium bicarbonate is dissolved (Solution A). In a separate flask, 18.0 g of sodium sulfate is dissolved in 500 mL of hot (˜80° C.) distilled water and boiled for 5 minutes (Solution B). Solution A is mixed with Solution B and the final volume is adjusted to 1000 mL by distill water. The reagent is stable for 2-3 months on storing in a dark glass vessel at room temperature.

The Nelson reagent is prepared as follows. 50 g of ammonium molybdate is dissolved in 900 mL of hot (˜60° C.) distilled water. The solution is cooled to 5-10° C. and 42 mL of concentrated sulfuric acid containing 6 g of sodium arsenate are carefully added with stirring. The volume of the mixture is adjusted to 1000 mL with distilled water. The flask with this solution is incubated at 40° C. for 48 hours and then the solution is filtered if necessary. The reagent is stable for 2-3 months at room temperature.

Using the above reagents, the assay is performed as detailed below.

Buffer Blank

0.2 mL of 0.05 M sodium acetate buffer (pH 5.0) is mixed in a graduated glass test tube with 0.2 mL of Somogyi reagent, covered, and incubated in a boiling water bath for 40 minutes. Then, the test tube is cooled in a cold-water bath and 0.2 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 2 mL with distilled water. The obtained solution is used as a buffer blank.

Determination of Avicelase Activity

Avicelase activity is determined by carrying out of the reaction of Avicel hydrolysis at 40° C. and pH 5.0 for 60 minutes while mixing. A 1% w/v stock suspension of Avicel is mixed on magnetic stirrer for 10 minutes, then 0.25 mL of this 1% w/v Avicel stock solution is placed in a graduated glass test tube. 0.15 mL of 0.05 M acetate buffer (pH 5.0) is added to the tube and the mixture is heated to 40° C. for 10 minutes with stirring. 0.1 mL of enzyme sample, suitably diluted and preheated to 40° C. for 10 minutes, is placed into the tube. The reaction mixture is then incubated for 1 hour at 40° C. with stirring. After 1 hour, the reaction mixture is centrifuged 2 min at 12000 rpm, 0.2 mL of supernatant is withdrawn and placed in a graduated glass test tube. 0.2 mL of Somogyi reagent is added and the mixture incubated, covered, in a boiling water bath for 40 minutes. Then, the tube is cooled in a cold water bath and 0.2 mL of Nelson reagent is added and mixed by shaking manually. After 1.0 minutes incubation at room temperature, the solution volume is adjusted to 2 mL with distilled water. Then, the absorbance at 610 nm (A₆₁₀) is measured against the buffer blank as A_(ES) (enzyme sample). The enzyme sample must be diluted with the 0.05 M sodium acetate buffer so that A₆₁₀ is between 0.5 and 1.5 units of optical density at 610 nm.

Enzyme Blank

0.16 mL of 0.05 M sodium acetate buffer (pH 5.0) is mixed in a graduated glass test tube with 0.04 mL of enzyme sample having the same dilution rate as above. 0.2 mL of Somogyi reagent is added to the test tube, and the tube is incubated, covered, in a boiling water bath for 40 minutes. Then, the test tube is cooled in a cold water bath, 0.2 mL of Nelson reagent is added and the tube is mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 2 mL with distilled water. Then, the absorbance at 610 nm (A₆₁₀) is measured against the buffer blank as A_(E) (enzyme blank).

Substrate Blank

A 1% w/v stock suspension of Avicel is mixed using a magnetic stirrer for 10 minutes, then 0.25 mL of the 1% w/v Avicel stock solution is placed into a graduated glass test tube. 0.25 mL of 0.05 M acetate buffer (pH 5.0) is added to the tube and the mixture is heated to 40° C. for 10 minutes with stirring. 0.1 mL of enzyme sample, suitably diluted and preheated to 40° C. for 10 minutes, is placed into the tube. The reaction mixture is then incubated for 1 hour at 40° C. with stirring. After 1 hour, the reaction mixture is centrifuged 2 min at 12000 rpm, 0.2 mL of supernatant is withdrawn and placed in a graduated glass test tube. 0.2 mL of Somogyi reagent is added and the mixture incubated, covered, in a boiling water bath for 40 minutes. Then, the tube is cooled in a cold water bath and 0.2 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 2 mL with distilled water. Then, the absorbance at 6.10 nm (A₆₁₀) is measured against the buffer blank as A_(S) (substrate blank).

Standard Calibration Plot

Stock glucose solution (0.5 mg/mL) is prepared by dissolving 10 mg of D-glucose in 20 mL of 0.05 M acetate buffer, pH 5.0. Then, different dilutions of stock glucose solution are prepared as follows:

0.05M acetate Stock solution (mL) buffer (mL) Glucose concentration (mg/mL) 0.020 0.180 0.02 0.040 0.160 0.04 0.060 0.140 0.06 0.080 0.120 0.08 0.100 0.100 0.10 0.120 0.080 0.12 0.140 0.060 0.14 0.160 0.040 0.16 0.180 0.020 0.18 0.200 0 0.20 Samples (0.2 mL) of glucose solution with different dilutions are placed to graduated glass test tubes. 0.2 mL of Somogyi reagent is added and the test tubes are placed into a boiling water bath for 40 minutes. Then, the test tubes are cooled in a cold water bath and 0.2 mL of Nelson reagent is added to each tube, and the tubes mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume in each tube is adjusted to 2 mL with distilled water. Then, the absorbance at 610 nm (A₆₁₀) is measured against the buffer blank. The following typical A₆₁₀ data obtained with different glucose dilutions are given below:

Glucose, mg/mL 0.02 0.04 0.06 0.08 0.10 0.12 0.14 0.16 0.18 0.20 A₆₁₀ 0.02 0.12 0.38 0.50 0.70 0.92 1.10 1.38 1.54 1.67 Absorbance (A₆₁₀) on the y-axis versus glucose concentration (G, mg/mL) on the x-axis is plotted to generate a standard calibration plot such as that shown in the FIG. 11.

The dependence of A₆₁₀ from G is described by the equation y=ax+b. The concentration of reducing sugars (C) in an assayed sample can be calculated from a calibration plot using the equation C=(ΔA₆₁₀−b)/a, where b=0.2239 and 1/a=0.204. In other words, C=(ΔA₆₁₀+0.223.9)*0.104 (in mg/mL).

Calculation of Activity

Activity is calculated as follows: Avicelase (U/mL)=(ΔA₆₁₀−b)*(l/a)*0.463*DR, where ΔA₆₁₀=A_(ES) (enzyme sample)−A_(E) (enzyme blank)−A_(S) (substrate blank), l/a is 0.204, b is −0.2239, the coefficients from the glucose calibration plot (see above), DR is the enzyme dilution rate (dilution rate of enzyme sample before addition into the reaction mixture), and 0.463 is the coefficient obtained as 5/(0.180*60), where 5 is the additional dilution of enzyme sample in the reaction mixture (0.1 mL of enzyme+0.4 mL of reaction mixture), 0.1.80 mg/mkmol is the transition coefficient for glucose from mg to mkmol (molecular weight of glucose is 1.80) and 60 is the reaction time (60 minutes). The enzyme sample must be diluted so that ΔA₆₁₀ should be between 0.5 and 1.5 units of optical density.

An example calculation is supplied below. The sample the dilution rate of 500. A_(ES) is 1.436, A_(E) is 0.102, A_(S) is 0.070, so ΔA₆₁₀=1.436−0.102−0.070=1.264. The Avicelase activity is: (1.264+0.2239)*0.104*0.463*500=35.8 U/mL.

Example 6

The following example illustrates glucose determination by a glucosooxidase-peroxidase assay.

As a result of β-D-Glucose oxidation by glucose oxidase (GOD), hydrogen peroxide H₂O₂ and glucono-lactone are formed. Then, H₂O₂ is used by peroxidase (POD) as an oxidizing agent for 4-aminoantipyrine, oxidizing in the presence of phenolic substances. As a result, dyed products accumulate in the reaction mixture and can be detected at 490 nm spectrophotometrically. The amount of dyed products corresponds to glucose concentration as shown in the reaction scheme below:

The assay is carried out using a Fotoglucose kit (Impact Ltd., Russia) with the general conditions: 40° C., pH 7.0, duration −15 min, A₄₉₀, light path 1 cm.

Reagents

Reagent 1 (R1) is prepared as follows. Two “Buffer-Substrate” tablets (0.1 mmol/L potassium or ammonium salts of phosphoric acid. 50 mmol/l 4-aminoantipyrine, 0.75 mmom/L 8-oxyquinolyn) are dissolved in 200 mL of distilled water, filtered through a cellulose filter, and the pH adjusted to 7.0 if necessary. The solution can be stored in the dark at 4° C. and should be made fresh weekly.

Reagent 2 (R2) is prepared as follows. One “Enzyme” tablet (2500 units of glucose oxidase and 500 units of peroxidase) is dissolved in 5 mL of distilled water. The solution can be stored in the dark at 4° C. and should be made fresh weekly.

A glucose solution of 10 mmol/L glucose in 0.15% benzoic acid is used as the calibration standard. The solution is diluted with distilled water to obtain glucose solutions of 0 to 5 g/L.

Using the above reagents, the assay is performed as detailed below.

R1 and R2 are mixed at a ratio of 40:1 (this solution may be stored in the dark at 4° C. and should be made fresh weekly) and 1 mL of the mixture is preheated to 40° C. for 5-10 seconds. 0.1 mL of the sample (or glucose standard) is then added and the mixture is incubated at 40° C. for 15 minutes. The mixtures are then placed at room temperature and the A₄₉₀ determined on spectrophotometer. Prolongation of the incubation time to 20 minutes has little or no effect on the results, while decreasing it to less than 15 minutes can result in a lower optical density. Thus, 15-20 min of incubation at 40° C. is preferred for glucose determination.

Calculation of Glucose Concentration

As shown in Table 21, calibration with standards containing varying concentrations of glucose reveals an optical density A₄₉₀ in the range from 0.06 to 1.15 corresponds to glucose concentrations from 0.025 μg/L to 0.5 g/L. These data are plotted in FIG. 12, which demonstrates a linear proportion and high reproducibility at these conditions.

Using the calibration results, the following formula is obtained for glucose determination in samples from an A₄₉₀ reading:

GLUCOSE, g/L=(A₄₉₀sample−A₄₉₀blank)−0.0058)/2.3029

TABLE 21 Calibration of the reagents using standard glucose solutions (two experiments) Glucose, g/L A₄₉₀ A₄₉₀ 0 0.05 0.05 0.0025 0.05 0.05 0.005 0.06 0.06 0.01 0.07 0.07 0.025 0.11 0.11 0.05 0.17 0.17 0.1 0.29 0.29 0.25 0.65 0.64 0.5 1.20 1.20 1 1.71 1.72 2.5 1.93 1.94 5 2.06 2.06

Example 7

The following example illustrates the Somogyi-Nelson assay used to measure xylanase activity.

This assay measures the release of reducing sugars (as glucose equivalents) by the action of xylanase on a soluble xylan. One xylanase unit of activity is the amount of enzyme that liberates 1 micromole of reducing sugars, expressed as glucose equivalents, in one minute at 50° C. and pH 5.0.

Reagents

Acetate buffer (0.05 M, pH 5.0) is prepared as follows. 4.1 g of anhydrous sodium acetate or 6.8 g of sodium acetate*3H₂O is dissolved in distilled water so that the final volume of the solution is 1000 mL (Solution A). In a separate flask, 3.0 g (2.86 mL) of glacial acetic acid is mixed with distilled water to make a total volume of 1000 mL (Solution B). The final 0.05 M acetate buffer, pH 5.0, is prepared by mixing Solution A with Solution B until the pH of the resulting solution is equal to 5.0.

Xylan from birchwood (Sigma, X 0502) is used as the substrate. A 1% w/v stock solution is prepared by dissolving 500 mg of xylan in 50 mL of distilled water with agitation on a magnetic stirrer for 1 hour. The solution is stable for 2 days at 4° C.

The Somogyi reagent is prepared as follows. 24 g of anhydrous sodium carbonate and 12 g of sodium-potassium tartrate tetrahydrate are dissolved in 250 mL of distilled water. A solution of copper sulfate pentahydrate (4 g in 40 mL of distilled water) is added with stirring, and then 16 g of sodium bicarbonate is dissolved to obtain Solution A. In a separate flask, 180 g of sodium sulfate is dissolved in 500 mL of hot (˜80° C.) distilled water and boiled for 5 min (Solution B). Solution A is mixed with Solution B and the final volume is adjusted to 1000 mL. The reagent is stable for 2-3 months on storing in a dark glass vessel.

The Nelson reagent is prepared as follows. 50 g of ammonium molybdate is dissolved in 900 mL of hot (˜60° C.) distilled water. The solution is cooled to 5-10° C. and 42 g of concentrated sulfuric acid containing 6 g of sodium arsenate are carefully added with stirring. The volume of the mixture is adjusted to 1000 mL. The flask is incubated at 40° C. for 48 hours and then the solution is filtered if necessary. The reagent is stable for 2-3 months.

Using the above reagents, the assay is performed as detailed below.

Reagent Blank

0.5 mL of 0.05 M sodium acetate buffer is mixed in a graduated glass test tube (1.5 cm×15 cm) with 0.5 mL of Somogyi reagent and incubated in a boiling water bath for 40 minutes. Then, the test tube is cooled in an ice or cold water bath and 0.5 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 5 mL with distilled water.

Enzyme Sample

0.25 mL of 1% w/v xylan stock solution is mixed with 0.15 mL of 0.05 M acetate buffer, pH 5.0, in graduated glass test tubes (1.5 cm×0.15 cm) and preheated at 50° C. for 5 minutes. Enzyme sample is suitably diluted by the 0.05 M sodium acetate buffer (the dilution of the enzyme sample is chosen so that A₆₁₀ should be between 0.95 and 1.05 units of optical density). 0.1 mL of suitably diluted enzyme sample is added to 0.4 mL of the preheated substrate solution, mixed and incubated at 50° C. for 10 minutes. After exactly 10 minutes of incubation, 0.5 mL of Somogyi reagent is added, and test tubes are placed into a boiling water bath for 40 minutes. Then, the test tubes are cooled in an ice or cold water bath and 0.5 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 5 mL with distilled water. Then, the absorbance at 6.1.0 nm (A₆₁₀) is measured against the reagent blank as A_(S) (enzyme sample).

Enzyme Blank

0.4 mL of 0.05 M sodium acetate buffer is mixed in a graduated glass test tube (1.5 cm×15 cm) with 0.1 mL of enzyme sample having the same dilution as above. 0.5 mL of Somogyi reagent is added and the test tube is incubated in a boiling water bath for 40 minutes. Then, the test tube is cooled in an ice or cold water bath and 0.5 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 5 mL with distilled water. Then, the absorbance at 610 nm (A₆₁₀) is measured against the reagent blank as A_(EB) (enzyme blank).

Substrate Blank

0.25 mL of 1% w/v xylan stock solution is mixed with 0.25 mL of 0.05 M acetate buffer, pH 5.0, in a graduated glass test tube (1.5 cm×15 cm), 0.5 mL of Somogyi reagent is added, and the test tube is placed into a boiling water bath for 40 minutes. Then, the test tube is cooled in an ice or cold water bath and 0.5 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 5 mL with distilled water. Then, the absorbance at 610 nm (A₆₁₀) is measured against the reagent blank as A_(SB) (substrate blank). The value of A_(SB) should not exceed 0.05 units of optical density.

All enzyme samples and enzyme and substrate blanks should be boiled together.

Standard Calibration Plot

Stock glucose solution (1 mg/mL) is prepared by dissolving 100 mg of D-glucose in 100 mL of 0.05 M acetate buffer, pH 5.0. Then, different dilutions of stock glucose solution are prepared as follows:

0.05M acetate Stock solution (mL) buffer (mL) Glucose concentration (mg/mL) 0.05 4.95 0.01 0.10 4.90 0.02 0.15 4.85 0.03 0.20 4.80 0.04 0.25 4.75 0.05 0.30 4.70 0.06 0.35 4.65 0.07 0.40 4.60 0.08 0.45 4.55 0.09 0.50 4.50 0.10 Samples (0.5 mL) of glucose solution with different dilutions are placed in graduated glass test tubes (1.5 cm×15 cm). 0.5 mL of Somogyi reagent is added and test tubes are placed into a boiling water bath for 40 minutes. Then, the test tubes are cooled in an ice or cold water bath and 0.5 mL of Nelson reagent is added and mixed by shaking manually. After 10 minutes incubation at room temperature, the solution volume is adjusted to 5 mL with distilled water. Then, the absorbance at 610 nm (A₆₁₀) is measured against the reagent blank. The following typical A₆₁₀ data obtained with different glucose dilutions are given below:

Glucose, mg/mL 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10 A₆₁₀ 0.11 0.20 0.28 0.41 0.48 0.60 0.72 0.79 0.93 1.06 Absorbance (A₆₁₀) on the y-axis versus glucose concentration (G, mg/mL) on the x-axis is plotted to demonstrate a standard calibration plot such as that shown in FIG. 11. From FIG. 11, the inverse of the slop (l/a=0.098) is calculated.

Calculation of Activity

Activity is calculated as follows: activity (IU/mL)=l/a*ΔA₆₁₀*DF*2.78, where l/a is the inverse of the slope calculated from the standard calibration plot, ΔA₆₁₀ is A_(S) (enzyme sample)−A_(EB) (enzyme blank)−A_(SB) (substrate blank), DF is the enzyme dilution factor, and 2.78 is the coefficient that accounts for additional 5-fold enzyme dilution in the reaction mixture (0.1 mL enzyme+0.4 mL substrate), reaction time (10 minutes) and molecular weight of glucose (0.18016 mg/micromole), i.e. 5/(10*0.18016)=2.78

An example calculation is supplied below.

B4 UF concentrate DF ΔA₆₁₀ 5,000 1.61 10,000 1.04 20,000 0.64 Xylanase activity (IU/mL)=0.098*1.04*10000*2.78=2833

Example 8

The following example illustrates the assay used to measure the stability of enzymes of the present invention to thermoshock.

The following assay determines the stability of enzymes after short-term treatment at elevated temperature (e.g. temperature of pelletization of animal feed). A solution of enzyme is incubated for approximately two minutes in a glass tube in a thermostat at 80° C. The gradual drop of enzyme activity is recorded over time and the resultant curve is used to determine how long the enzyme is stable (results usually range from 1.0-60 seconds).

The use of glass tubes that fit tightly in a regular thermostat or eppendorf-type tubes help ensure proper thermal conditions and fast heating of the tube content. The enzyme dilution used is selected so that after additional dilution in reaction mixture the optical density is as high as possible (depends on particular method used for activity determination). For example, when determining xylanase activity by the Somogyi-Nelson assay disclosed in Example 7, the enzyme selected should give an optical density A₆₁₀ 1.0-1.1 after being diluted 5 times in reaction mixture.

For faster equilibration at 80° C., 0.4-0.5 ml water may be placed in the well of thermostat, prior to fitting in a glass tube. The temperature is set at 80.3-80.4° C. to compensate for cooling. 360 •l of desired buffer is placed in the tube and heated for 2-3 minutes until it reaches 80° C. It is advisable to check the temperature in the tube (using a thermometer) to be sure the temperature has been reached. 40•l of enzyme solution is then added and the tube is mixed rapidly. After 20, 40, 60, 90 and 120 seconds, aliquots are removed from the tube and immediately transferred in the reaction mixture for determination of activity (assay components are prepared beforehand). To determine zero-point activity (without heating), the same solution (360 •l buffer+40 •l enzyme) is prepared in the separate tube at room temperature. Determined activities at every time point are then plotted as relative activity (in %) vs. time, with zero time point (without heating) representing 100% activity. FIG. 13 demonstrates these data for stability of xylanase at 20-, 10- and 5-fold dilutions.

In this protocol, a 10-fold dilution of enzyme is used (9:1 preheated buffer solution to cold enzyme solution). In principle one can use higher dilution rates (e.g., 1:20), but typically not lower dilution factors (e.g., 1:5) because mixing of larger volumes of cold enzyme solution can produce inaccurate results. The plot below illustrates this principle. The stability of xylanase was tested using 20-, 10- and 5-fold dilutions, and the results shown in FIG. 13 demonstrate that dilutions of 10- and 20-fold (and likely higher) gave consistent results. In contrast, use of a 5-fold dilution generates overestimated values.

The percentages of enzymatic activity of xylanases of the present invention after 20 seconds of incubation at 80° C. (also known as the pelletizing stabilities) are shown below in Table 22 and in the graph depicted in FIG. 14.

TABLE 22 Pelletizing Stability of C1 Xylanses Enzyme % Activity Xyl 1 19 Xyl 1 (CD) 12 Xyl 2 98 Xyl 3 75 Xyl 3 (CD) 82 Xyl 4 23 Xyl 5 60 Xyl 6 68

Example 9

The following example illustrates the in vitro, semi-quantitative assay used to measure the feed activity of enzymes of the present invention.

The assay was developed to simulate the enzymatic treatment of feed. The assay detects the dynamics of liquid and sludge fraction formation from a uniform slurry of milled rye bran by the action of the enzyme samples in narrow test tubes.

A mixture of enzyme solution and uniform rye bran suspension in acetate buffer (pH 5.0) is placed into a long glass tube (e.g., 2 ml calibrated glass pipettes) and stored at room temperature (or at 40° C.). The action of enzymes on non-starch rye bran generates polysaccharides (e.g. arabinoxyan, β-glucan and others) causing the original uniform rye bran slurry to separate into a liquid phase (containing the polysaccharides) on the top and an insoluble sludge on the bottom of. The volume of liquid phase formed on the top of tubes over the reaction is measured every 10-15 min during 1.5-3 hours (the total assay time depends on enzymatic activity). The data obtained are plotted as “liquid formed” (ml) versus time (minutes) and the slope of the line calculated. The higher the slope of the line on the obtained graph, the higher the in vitro feed activity of the tested enzyme sample.

Substrate

Rye bran is used as a substrate in this example. However, wheat and barley bran, rye, wheat, barley, and soy meal may also be used as assay substrates. Partially de-starched rye bran samples are carefully milled and passed through the fine sieve. The fine fraction is taken as the substrate. Substrate is accurately weighed and placed into a dry 20-ml screw cap vial. The sample of substrate is suspended in acetate buffer to get 30% w/v suspension. The substrate suspension is mixed vigorously with a magnetic stirrer for 30-45 minutes at room temperature. The resulting suspension obtained can be stored at 4° C. in a sealed vial for about 2 days.

Assay Procedure

The reaction mixture contains the following components:

-   -   1500 μl of substrate suspension (300 mg/ml)     -   750 μl of enzyme solution

The blank solution contains the same amount of substrate, but the enzyme solution is substituted with the same volume of acetate buffer.

The reaction mixture is subjected to vigorous agitation and placed in appropriate calibrated glass tubes (e.g., 2 ml glass pipettes). Glass tubes or pipettes should be filled with the reaction mixture immediately and placed vertically. The top end of the tube is left open while the bottom end is sealed with a piece of Parafilm or by dipping in melted paraffin.

The concentration of enzyme samples can be measured either in mg/ml of protein or in xylanase units/ml in the reaction mixture (or any other enzyme activities, e.g., β-glucanase, α-galactosidase, protease, etc.). Protein content or xylanase (or other activities) of the enzyme samples are measured separately prior to the experiments. In the experiments, enzyme concentration was equalized to 1 mg/ml of protein in the reaction mixture, or in xylanase activity (2 to 3 U/ml).

Materials and Instruments

-   -   Thermostat for 2 ml Eppendorf type test tubes, set at 40° C.     -   Set of calibrated glass tubes (e.g., 2-ml glass pipettes)     -   UV-Vis spectrophotometer     -   Reagents to perform Nelson-Somogyi assay     -   Analytical electronic balances     -   Adjustable volume automated pipettes 40-200 μl and 200-1000 μl     -   Rye bran     -   0.05 M acetate buffer, pH 5.0

Data Analysis

Data obtained is presented on a graph as liquid formed (ml) versus time (minutes). The higher the slope of the line on the obtained graph, the higher the in vitro feed activity of the tested enzyme sample.

Example 10

The following example illustrates the assay used to measure the ability of enzymes to reduce the viscosity of feed materials.

Enzymatic treatment of barley, rye or wheat can increase the nutritive value by hydrolysis of viscous polysaccharides (beta-glucan, arabino xylan) within cereals. Table 23 below illustrates typical viscous polysaccharide profiles of sample feedstuffs compared with the viscosity of water/meal mixtures.

TABLE 23 Viscous Polysachharide Profiles of Feedstuffs Arabino Xylans Beta-Glucans, Relative Viscosity g/kg of dry g/kg of dry of water/meal matter matter mixes, U RYE 14.4 7.6 9.71 BARLEY 3.3 24.3 4.21 WHEAT 3.2 5.6 2.25

As shown in the table, the high viscosity of a water/rye meal mixture is predominantly due to the presence of arabinoxylans. Similarly, the viscosity of a water/barley mixture is predominantly due to the presence of beta-glucans, while the viscosity of water/wheat mixture close to water. However, cereals such as barley, rye and wheat often contain specific inhibitors of the hydrolytic enzymes. Thus, preferred enzymatic preparations that effectively decrease viscosity should be resistant to cereal inhibitors and be enzymatically active at low dosage.

Materials and Instruments

-   -   100 ml glass flasks with caps     -   Ostwald capillary viscometer with thermostat at 40° C.     -   Shaker for meal incubation at 40° C.     -   Whole rye, barley, wheat grains or hulls or their mixtures     -   Rotary mill and 0.5 mm sieve to prepare whole meal     -   Adjustable volume automated pipettes 40-200 and 200-1000 ul     -   Distilled water or 0.1 M sodium acetate buffer, pH 5.0

Sample Preparation

To prepare the crude barley, wheat or rye meals, whole grains are milled on a rotary mill and passed through a 0.5 mm sieve. 6 g of crude barley or rye meal or 12 g of wheat meal is added to a 100 ml glass flask. 30 ml of distilled water or buffer (blank flask) or 30 ml of the enzyme water solution (experimental flasks) is then added and the flasks are covered. The concentration of 6 g of meal per 30 ml of water is 200 g per liter, while 12 g per 30 ml is 400 g/l.

The flasks are shaken well by hand then placed on a shaker at 40° C., 250 rpm.

After a 1-hour incubation, the mixtures are centrifuged for 5 min at 5000 rpm to separate the insoluble precipitate of the crude meal. The supernatant is then filtered through a cotton pad. 5 ml of the filtered supernatant is placed into an Ostwald viscometer at 40° C. and incubated for at least 3 minutes before the viscosity of the sample is determined. The measurement of the efflux time of the samples from the viscometer bulb should be done later than 80 minutes after starting the incubation.

A dosage of 0.15 kg/t of the meal approximates the dosage used in real practice. For liquid preparations, a dosage of 0.15 kg/t equals 90 μl of the preparation in a 100-fold dilution per flask (30 ml of water/meal mix). For dry preparations, a dosage of 0.15 kg/t equals 90 μl of the 10 g/l solution per flask (30 ml of water/meal mix).

FIG. 15 shows the relative viscosity of water/rye mixes treated with the indicated enzyme(s). To compare the efficiency of the preparations, the xylanase activities of the samples (units per flask) are also indicated.

The efficiency of the preparations may also be compared by plotting the residual viscosity (%) of the water/meal mix after enzymatic treatment, as shown in FIG. 16.

Residual viscosity is calculated as follows:

ResV=(Rvi−Rvwater)/(Rvnative−Rvwater)×100%

The final formula is:

ResV=(Rvi−1)/(Rvnative−1)×100%

Where ResV is residual viscosity, Rvi is the relative viscosity of the sample with enzyme, Rvnative is the relative viscosity of the native water/meal mix without enzyme, and Rvwater is 1.

Table 24 shows of the residual viscosity (%) of rye meal water extract after a 1-hour incubation with 1 unit of the xylanases of the present invention. These data are presented graphically in FIG. 17.

TABLE 24 Residual Feed Viscosities of C1 Xylanses Enzyme % Residual Viscosity Xyl 1 59 Xyl 1 (CD) 59 Xyl 2 27 Xyl 3 25 Xyl 3 (CD) 76 Xyl 4 77 Xyl 5 94 Xyl 6 91

Table 25 shows of the residual viscosity (%) of barley meal after a 1-hour incubation with 1 unit of the endoglucanases of the present invention.

TABLE 25 Residual Feed Viscosities of C1 Endoglucanases Enzyme % Residual Viscosity EG I 18 EG II 13 EG II (CD) 14 EG III 10 EG V 18 EG VI 20

Example 11

The following example illustrates an assay used to measure the biobleaching ability of enzymes of the present invention.

Ability of different crude enzyme preparations or purified enzymes to (bio)bleach cellulosic pulp may be evaluated by the assay below. The assay monitors the release of chromogenic phenolic substances from raw cellulosic pulp by the action of enzymes. The phenolic substances are detected by the absorbance at 237 nm (A₂₃₇) or 235 nm (A₂₃₅).

Mini Biobleaching Assay

Raw (wet) eucalyptus cellulosic pulp with natural pH 7.7 (National Paper Fabric, Uruguay) is placed into 5 ml reaction tubes, and the tubes are placed into a water bath shaker, (50° C., 200 rpm). The reaction volume consists 2 ml of enzyme sample appropriately diluted in appropriate buffer solution and 2 ml of cellulosic pulp suspension (0.04 g of cellulosic pulp by dry weight). The concentration of cellulosic pulp is 10 mg/ml. The biobleaching process is started by the addition of 2 ml of enzyme solution to the pulp and the assay is conducted for 2 hours. After that reaction, the mixture is centrifuged and A₂₃₇ of the supernatant is monitored in a spectrophotometer. Since some phenolic compounds are washed out from the raw cellulosic pulp even in the absence of enzymes, the blank experiments with buffer solution only (with no enzymes) are carried out. Some input to A₂₃₇ value could be made by chromogenic substances, existing in the raw enzyme sample, so another blank experiments were carried out to estimate this input. All results take into account both of those blanks as ΔA₂₃₇. The higher the ΔA₂₃₇ value, the better was biobleaching performance.

The assay may also be performed using soft or hard wood pulp at pH 7.5 and 50° C. for 2 hours, with the absorbance determined at 235 nm. Table 26 and FIG. 18 show the biobleaching ability (A₂₃₅) of xylanases of the present invention on soft wood pulp under these conditions, while Table 27 and FIG. 19 show the same biobleaching ability on hard wood pulp. For each xylanase, the assay was conducted using 0.01, 0.003, 0.001, 0.0003 mg/ml of enzyme in the reaction mixture, as indicated. A positive control xylanase preparation (Luminase, Verenium Corp., San Diego, Calif. USA) was also used for comparison.

TABLE 26 Biobleaching Ability of C1 Xylanases on Soft Wood Pulp (A₂₃₅) Enzyme (mg/ml) Xyl 1 Xyl 3 (CD) Xyl 1 Xyl 3 (CD) Xyl 4 Xyl 2 Xyl 6 Luminase 0.01 3 1.37 2.28 2.2 1.73 3.66 2.62 3 0.003 2.65 1.015 2.7 1.43 1.1 2.8 2.03 2.445 0.001 2.385 1.07 0.85 1.05 0.455 2.22 1.7 2.14 0.0003 1.45 0.615 0.575 0.31 0.2 1.615 1.4 1

TABLE 27 Biobleaching Ability of C1 Xylanases on Hard Wood Pulp (A₂₃₅) Enzyme (mg/ml) Xyl 1 Xyl 3 (CD) Xyl 1 Xyl 3 (CD) Xyl 4 Xyl 2 Xyl 6 Luminase 0.01 8.5 2.355 4.2 3.715 1.9 5 6.5 7.585 0.003 6.25 1.82 2.24 2.27 0.82 4.45 4.5 5.6 0.001 5.4 1.37 1.05 1.5 0.5 2.355 3 4.8 0.0003 3.5 0.4 0.61 0.675 0.3 1.5 1.26 2.785

Example 12

The following example illustrates the Saccharification of pretreated lignocellulosic feedstock using crude enzyme preparations.

The assay involves a protocol for enzymatic saccharification of pretreated lignocellulosic biomass with a known moisture content and composition in order to determine the extent of cellulose and hemicellulose digestibility under concrete conditions of saccharification of the feedstock with crude cellulase and hemicellulase enzyme preparations.

Equipment

-   -   INNOVA 40 Thermo Shaker (New Jersey, USA), where agitation of a         slurry in plastic vessels is carried out using 250 rpm         vibrations (each vessel supplied by one 0.5 cm metal ball to         improve mixing of slung)     -   Micro centrifuge     -   pH meter     -   Vortex mixer     -   Analytical balance, sensitive to 0.1 mg     -   UV/Vis spectrophotometer     -   HPLC with refractive index detector and Silica column with         bonded amino phase (4×250 mm) and guard column     -   Pipettes with variable sample volume (5-5000 μL)

Reagents and Materials

-   -   Lignocellulosic feedstock with known moisture content and         composition (cellulose, hemicellulose, lignin, ash, extractives)     -   Sodium acetate buffer (0.1 M, pH 5.0) containing 1 mM of sodium         azide to prevent microflora growth     -   Enzyme cellulase and hemicellulase preparations from different         fungal strains, either in soluble or in dry form     -   Reagents for protein determination (either Lowry or Pierce BCA         kit)     -   Water, distilled and/or deionized     -   Ampiox, sodium-salt.     -   “Fotoglucose” kit (reagents for glucose determination using         glucose oxidase-peroxidase assay) from Impact Ltd., Russia     -   Somogyi and Nelson reagents for reducing sugars' assay     -   Acetonitrile, HPLC grade     -   NaOH, acetic acid for pH adjustments

Assay Procedure

The procedure described below assumes that the hydrolysis is carried out at 5% solids. If the process should be carried out at different substrate concentration, then recalculations should be done for the initial biomass sample weight (on a thy weight basis) using the known moisture content in the sample.

A biomass sample containing 1 g of solids (on a thy weight basis) is weighed and placed into a 50 ml plastic vessel equipped with a hermetic lid and one metal ball (0.5 cm in diameter) to improve mixing (the moisture content is determined in preliminary experiments by drying the biomass samples at 105° C. until a constant weight is reached). The weight (volume) of water in the sample is noted as W_(s).

The volume(s) of enzyme(s) necessary to add to the reaction mixture is calculated taking into account the protein concentration (enzyme activity) in a stock solution and the final protein concentration (enzyme activity) in the reaction mixture. Using these data, the volume of buffer (W_(a)) that is necessary for adjusting the total volume of the reaction system to 20 ml is calculated, taking into account water contained in the biomass sample (W_(s)).

The calculated amount (W_(a)) of 0.1 M, pH 5.0 Na-acetate buffer containing 200 mg/l (4 mM) of sodium azide is added to the biomass slurry, and the slurry is thoroughly mix in the 50 ml vessel using a Vortex. The pH is measure and adjusted pH to 5.0 using concentrated acetic acid or NaOH, if necessary. The lid is closed and the vessels incubated in an INNOVA 40 Thermo Shaker for 15 minutes to preheat the sample to 50° C.

The calculated amount(s) of enzyme stock solution(s) is added to the reaction mixture to start the enzymatic reaction. 20 μl of Ampiox solution (100 g/l) is then added to the final reaction mixture, which is allowed to proceed for 72 hours. (50° C. and 250 rpm vibrations).

Aliquots of the reaction slurry (50-100 μL) are typically taken at 6, 24, 48, 72 or 96 hour time points, using a pipette with a cut tip. The aliquots are centrifuged at 15,000 rpm in a micro centrifuge for 3 minutes, and the supernatants are analyzed for glucose by the glucose oxidase-peroxidase assay (see Example 6) and for reducing sugars by the Nelson-Somogyi assay (see, for example, Example 1). Samples (supernatants) are typically analyzed immediately. In some cases, they are subjected to boiling for 5 minutes, then frozen and analyzed later. The final time point (72 hours) is also analyzed for sugars by HPLC.

A substrate blank (control) is prepared in the same way as described above, except that distilled water is added to the vessel instead of the enzyme(s) stock solution(s). The supernatant resulting from the substrate blank is analyzed for glucose by the glucose oxidase-peroxidase assay, reducing sugars by the Nelson-Somogyi assay and also for sugars by HPLC.

Reactions are typically carried out in duplicate. The results of the analysis for sugars are determined, as average values together with standard deviations. Typically, the protein content in the reaction system (mg protein/g solids) is used as a measure of enzyme loading. In the experiments with crude enzyme preparations, the enzyme loading is 5, 2.5 and 1 mg protein/g solids. In enzymatic reactions may be carried out in the presence of β-glucosidase preparations (40 Units of p-NPh-β-glucosidase activity per 1 g solids) in order to convert all soluble oligosaccharides to glucose.

Calculations

To calculate the percent digestibility of cellulose (glucan), the glucose concentration in the final (72 or 96 hour) supernatant of the reaction mixture is determined (data from the glucose oxidase-peroxidase assay and/or HPLC assay), subtract the glucose concentration from the substrate blank (control). The initial cellulose (glucan) content in the reaction system is also calculated. For example, if the cellulose content in the pretreated feedstock is 35% of the total solids (dry matter) and the hydrolysis is carried out at 100 g solids/L, then the initial cellulose concentration would be 35 mg/mL.

The percent digestion of cellulose is calculated as follows:

${{Digestion}\mspace{14mu} (\%)} = \frac{{Glucose}\mspace{14mu} {concentration}\mspace{14mu} \left( {{mg}\text{/}{mL}} \right) \times 100\%}{{Initial}\mspace{14mu} {cellulose}\mspace{14mu} {concentration}\mspace{14mu} \left( {{mg}\text{/}{mL}} \right) \times 1.11}$

The factor 1.11 is a result of hydration of anhydroglucose residues in cellulose (162 Da per one residue) that yields a glucose molecule (1.80 Da).

To calculate the percent digestibility of hemicellulose (xylan), the total concentration of pentoses (xylose+arabinose) in the final (72 or 96 hour) supernatant of the reaction mixture is determined (data from HPLC assay), subtracting the pentose (xylose+arabinose) concentration from the substrate blank (control). The initial hemicellulose (xylan) content in the reaction system is also calculated. For example, if hemicellulose content in the pretreated feedstock is 30% of the total solids (dry matter) and the hydrolysis is carried out at 100 g solids/l, then the initial hemicellulose concentration would be 30 mg/ml.

The percent digestion of hemicellulose is calculated as follows:

${{Digestion}\mspace{14mu} (\%)} = \frac{{Total}\mspace{14mu} {pentose}\mspace{14mu} {concentration}\mspace{14mu} \left( {{mg}\text{/}{mL}} \right) \times 100\%}{{Initial}\mspace{14mu} {hemicellulose}\mspace{14mu} {concentration}\mspace{14mu} \left( {{mg}\text{/}{mL}} \right) \times 1.136}$

The factor 1.136 is a result of hydration of anhydropentose (xylose or arabinose) residue in hemicellulose (132 Da per one residue) that yields a pentose molecule (150 Da).

REFERENCES

-   1. Berezin I V, Rabinovich M L, Sinitsyn A P (1977) Study of     applicability of quantitative kinetic spectrophotometric method for     glucose determination. Biokhimiya (Moscow) 42:1631-1636. -   2. Chose T K (1987) Measurement of cellulase activities. Pure Appl.     Chem. 59:257-268. -   3. Gusakov A V, Salanovich T N, Antonov A L Ustinov B B, Okunev O N,     Burlingame R, Emalfarb M, Baez M. Sinitsyn A P (2007) Design of     highly efficient cellulase mixtures for enzymatic hydrolysis of     cellulose. Biotechnol. Bioeng. On-line:     http://www3.interscience.wiley.com/cgi-bin/abstract/114064699/, DOI:     10.1002/bit.21329 -   4. Lowry O H, Rosebrough N J, Farr A L, Randall R J (1951) Protein     measurement with the Folin phenol reagent. J. Biol. Chem.     193:265-275. -   5. Sinitsyn A P. Chemoglazov V M. Gusakov A V (1990) Methods of     investigation and properties of cellulolytic enzymes (in Russian),     Biotechnology Series, v.25. Moscow: VINITI Press. 220 p. -   6. Somogyi M (1952) Notes on sugar determination. J. Biol. Chem.     195:19-23.

Example 13

The following example illustrates the saccharification of pretreated lignocellulosic feedstock with individual purified enzymes and enzyme mixtures.

The assay involves a protocol for the enzymatic saccharification of pretreated lignocellulosic biomass with known moisture content and composition in order to determine the extent of cellulose and hemicellulose digestibility under concrete conditions of saccharification of the feedstock with individual purified enzymes (monocomponents) and their compositions (mixes of monocomponents).

Equipment

-   -   TS-100 Thermo Shaker (Riga, Latvia), where agitation of a slurry         in plastic tubes is carried out using 1200 rpm vibrations     -   Micro centrifuge     -   pH meter     -   Vortex mixer     -   Analytical balance, sensitive to 0.1 mg     -   UV/Vis spectrophotometer     -   HPLC with refractive index detector and Silica column with         bonded amino phase (4×250 mm) and guard column     -   Pipettes with variable sample volume (5-1000 μL)

Reagents and Materials

-   -   Lignocellulosic feedstock with known moisture content and         composition (cellulose, hemicellulose, lignin, ash, extractives)     -   Sodium acetate buffer (0.1 M, pH 5.0) containing 1 mM of sodium         azide to prevent microflora growth     -   Enzyme monocomponents (cellulases, hemicellulases, glycosidases)         isolated from different fungal strains, either in solution or         freeze-dried     -   Reagents for protein determination (either Lowry or Pierce BCA         kit)     -   Water, distilled and/or deionized     -   “Fotoglucose” kit (reagents for glucose determination using         glucose oxidase-peroxidase assay) from Impact Ltd., Russia     -   Somogyi and Nelson reagents for reducing sugars' assay     -   Acetonitrile, HPLC grade     -   NaOH, acetic acid for pH adjustments.

Assay Procedure

The procedure described below assumes that the hydrolysis is carried out at 10% solids. If the process should be carried out at different substrate concentration, then recalculations should be done for the initial biomass sample weight (on a dry weight basis) using the known moisture content in the sample.

A biomass sample containing 200 mg of solids (on a dry weight basis) is weighed and placed into a 2 nil plastic tube equipped with a hermetic lid (the moisture content is determined in preliminary experiments by drying the biomass samples at 105° C. until a constant weight is reached). The weight (volume) of water in the sample is noted as W_(s).

1 ml of Na-acetate buffer (0.1 M, pH 5.0) containing 1 mM of sodium azide is added, and the slurry is thoroughly mixed using a vortex. The pH is measured and adjusted to 5.0 using concentrated acetic acid or NaOH, if necessary.

The volume(s) of enzyme(s) that is necessary to add to the 2 ml tube is calculated, taking into account the protein concentration (enzyme activity) in a stock solution and the final protein concentration (enzyme activity) in the reaction mixture. Using these data, the volume of water (buffer), that is necessary for adjusting the total volume of the reaction system to 2 mL (W_(a)) is calculated, taking into account water contained in the biomass sample (W_(s)) and the previously added 1 ml of buffer.

The calculated amount of the acetate buffer (W_(a)) is added to the biomass slurry, the lid closed and the tube incubated in a TS-100 Thermo Shaker for 5 minutes to preheat the sample to 50° C. The calculated amount(s) of enzyme stock solution(s) is added to the tube to start the enzymatic reaction. The reaction is allowed to proceed at 50° C. and 1200 rpm vibrations in a TS-100 Thermo Shaker for 96 hours.

Aliquots of the reaction slurry (50-100 μL) are typically taken at 3 or 6, 24, 48, 72, and 96 hours, using a pipette with a cut tip. The aliquots are centrifuged at 15.000 rpm in a micro centrifuge for 3 minutes, and the supernatants are analyzed for glucose by the glucose oxidase-peroxidase assay (see Example 6) and for reducing sugars by the Nelson-Somogyi assay (see, for example. Example 1). Samples (supernatants) are typically analyzed immediately. In some cases, they are boiled for 5 minutes, frozen and analyzed later. The final time point (96 hours) is also analyzed for sugars by HPLC.

A substrate blank (control) is prepared in the same way as above, except that distilled water is added to the tube instead of the enzyme(s) stock solution(s). The supernatant resulting from the substrate blank is analyzed for glucose by the glucose oxidase-peroxidase assay, reducing sugars by the Nelson-Somogyi assay and also for sugars by HPLC. Typically, there is no need to prepare enzyme blanks since purified enzymes (monocomponents) usually don't contain sugars.

All reactions are carried out in duplicate, and the results of the analysis for sugars are given as average values together with standard deviations. Typically, protein content in the reaction system (mg protein/g solids) is used as a measure of enzyme loading. In the case of purified enzymes where the amino acid sequences are known, the protein concentration is calculated from the UV absorption at 280 nm using enzyme extinction coefficients predicted by the ProtParam tool (http://www.expasy.ch/tools/protparam.html). Otherwise, the protein concentration is determined using the Lowly (Pierce BCA) assay.

In the experiments with individual purified enzymes (monocomponents), the enzyme loading is 2 mg protein/g solids. In the case of monocomponent cellulases (endoglucanases and cellobiohydrolases), the enzymatic reactions are carried out in the presence of purified β-glucosidase (0.5 U/ml cellobiase activity) in order to convert all soluble oligosaccharides to glucose.

In the experiments with mixes of monocomponents, the enzyme loading is typically 2 mg of total protein per 1 g of solids, when preliminary screening of mixes is carried out. With selected mixes of monocomponents, the enzyme (protein) loading may be varied (up to 5-10 mg protein/g solids).

Calculations

To calculate the percent digestibility of cellulose (glucan), the glucose concentration in the final (96 hour) supernatant of the reaction mixture is calculated (data from the glucose oxidase-peroxidase assay and/or HPLC assay), subtract the glucose concentration from the substrate blank (control). The initial cellulose (glucan) content in the reaction system is also calculated. For example, if the cellulose content in the pretreated feedstock was 35% of the total solids (dry matter) and the hydrolysis was carried out at 0.100 g solids/l, then the initial cellulose concentration would be 35 mg/ml.

The percent digestion of cellulose is calculated as follows:

${{Digestion}\mspace{14mu} (\%)} = \frac{{Glucose}\mspace{14mu} {concentration}\mspace{14mu} \left( {{mg}\text{/}{mL}} \right) \times 100\%}{{Initial}\mspace{14mu} {cellulose}\mspace{14mu} {concentration}\mspace{14mu} \left( {{mg}\text{/}{mL}} \right) \times 1.11}$

The factor 1.11 is a result of hydration of anhydroglucose residue in cellulose (162 Da per one residue) that yields a glucose molecule (1.80 Da).

To calculate the percent digestibility of hemicellulose (xylan), the total concentration of pentoses (xylose+arabinose) in the final (96 hour) supernatant of the reaction mixture is determined (data from HPLC assay), subtract the pentose (xylose+arabinose) concentration from the substrate blank (control). The initial hemicellulose (xylan) content in the reaction system is also calculated. For example, if the hemicellulose content in the pretreated feedstock is 30% of the total solids (dry matter) and the hydrolysis is carried out at 1.00 g solids/l, then the initial hemicellulose concentration would be 30 mg/ml.

The percent digestion of hemicellulose is calculated as follows:

${{Digestion}\mspace{14mu} (\%)} = \frac{{Total}\mspace{14mu} {pentose}\mspace{14mu} {concentration}\mspace{14mu} \left( {{mg}\text{/}{mL}} \right) \times 100\%}{{Initial}\mspace{14mu} {hemicellulose}\mspace{14mu} {concentration}\mspace{14mu} \left( {{mg}\text{/}{mL}} \right) \times 1.136}$

The factor 1.136 is a result of hydration of anhydropentose (xylose or arabinose) residue in hemicellulose (132 Da per one residue) that yields in pentose molecule (150 Da).

REFERENCES

-   1. Berezin I V, Rabinovich M L, Sinitsyn A P (1977) Study of     applicability of quantitative kinetic spectrophotometric method for     glucose determination. Biokhimiya (Moscow) 42:1631-1636. -   2. Ghose T K (1987) Measurement of cellulase activities. Pure Appl.     Chem. 59:257-268. -   3. Gusakov A V, Salanovich T N, Antonov A I, Ustinov B B, Okunev O     N, Burlingame R, Emalfarb M, Baez M, Sinitsyn A P (2007) Design of     highly efficient cellulase mixtures for enzymatic hydrolysis of     cellulose. Biotechnol. Bioeng. On-line:     http://www3.interscience.wiley.com/cgi-bin/abstract/114064699/, DOI:     1.0.1002bit.21329 -   4. Lowry O H, Rosebrough N J, Farr A L, Randall R J (1951) Protein     measurement with the Folin phenol reagent. J. Biol. Chem.     193:265-275. -   5. Sinitsyn A P, Chemoglazov V M, Gusakov A V (1990) Methods of     investigation and properties of cellulolytic enzymes (in Russian),     Biotechnology Series, v.25. Moscow: VINITI Press. 220 p. -   6. Somogyi M (1952) Notes on sugar determination. J. Biol. Chem.     195:19-23.

Example 14

The following example illustrates an assay used to measure the thermal stability of enzymes of the present invention.

This assay allows the determination of the long-term thermal stability of an enzyme at 40, 50 and 70° C. and at different pH values (the preferred values may vary with the area of use of the enzyme and its pH-profile, which is typically from pH 5.0 or 7.0). A solution of enzyme is incubated from 3-24 hours in a thermostat. The gradual drop of enzyme activity is recorded. The resulting data are used to determine enzyme half-life or enzyme activity after 3 hours of incubation under specified conditions (temperature and pH).

An enzyme dilution that gives a high enough optical density to be determined when the enzyme is diluted (e.g., in the range 0.8-1.2 using the Somogyi-Nelson assay described above) should be selected. 500-800 μl of this dilution (prepared using preheated buffer and 10- to 20-fold dilution factors (e.g., 450 μl preheated buffer+50 μl of enzyme)0 is placed into a 1.5-2.0 ml eppendorf tube (capped) in a thermostat set at 40, 50 or 60° C. Aliquots are removed at 15, 30, 45, 60, 90, 120, 180 minutes and activity determined simultaneously using any of the enzyme activity assays disclosed in this application or known in the art. A zero-point activity is determined by preparing the same enzyme dilution at room temperature. Relative activity (in %) is plotted versus time, with the activity of the enzyme at the zero-time point (without heating) set to 100%.

Example 15

The following example illustrates methods of bioscouring textiles using enzymes of the present invention.

The methods below are primarily intended for testing small amount of enzymes (mini-testing in the range of 0.5-5 mg of enzyme sample).

Bioscouring Assays

Scouring removes hydrophobic waxes and pectic substance from the surface of raw cotton fabric. The following methods, which allow the evaluation of the scouring efficiency of pure enzymes and crude enzyme preparations, are listed below:

-   1) Scouring and evaluating procedure for strips of 2.5×16 cm textile     strips, -   2) Micromethod of scouring and evaluating procedure for circular     pieces of textile, diameter 1.4 cm, -   3) Method for determination (staining) of remaining pectic     substances in scoured textile (qualitative), -   4) Method for determination of remaining waxes in scoured textile.

Method A. Scouring and Evaluation Procedure for the Strips of 2.5×16 Cm Textile Strips

Sample preparation: For all testing, raw weave 100% cotton fabric is used (density of 142 g/m²). Cotton fabric is desized by α-amylase overnight with surfactant added at room temperature, then rinsed and dried at room temperature. For 1-2 m² fabric, about 5 liters of solution containing 5 g/l textile α-amylase preparation and 1 g/l nonionic surfactant for scouring is needed. The fabric is rinsed thoroughly with tap water and dried at room temperature overnight. The fabric should not be ironed. The fabric is then cut into strips (2.5×16 cm).

Scouring procedure: The strips are treated in 100 mL plastic vessels on an Elpan water bath shaker at 50° C. at 250 rpm for one hour. Two 16×2.5 cm strips of fabric (1.1-1.2 g total) are loaded in one vessel. The liquor ratio is 20:1, using 0.1M acetate buffer, pH 5.0.

In detail, the strips, usually 20 strips (in 10 vessels), are marked with a textile marker, then dipped into the water to completely wet each strip. An enzyme solution (20 ml) is poured in the vessels. Then, two wet strips are rapidly placed into each vessel using tweezers. The vessels are capped and placed into a preheated water bath shaker (set at 50° C. 250 rpm, amplitude 4) for one hour.

After the treatment, the strips are rinsed with cold tap water for 2-4 minutes, usually in one bath, and then dried at room temperature overnight. More intense rinses have been tested (hot water, sequestrates e.g. EDTA, surfactants) but are not recommended since they provide less reproducible results.

Heating: Dry strips are heated for 1 hour at 105° C., allowed to remain overnight at room temperature, and then assayed for wicking height.

Analysis of wettability: Wettability (wicking height) is measured according to the Russian textile standard. One end of the vertical strip of dry fabric is immersed in a water bath. Wicking height (cm) is measured after 30 minutes. The higher the value of wicking height—the better the scouring result. A value of 8 cm or higher (for heated samples) indicates good scouring. All experiments are conducted in duplicate or triplicate.

Enzyme dosages for commercial preparations are usually within the range 5-60 g preparation per kg textile. Preferably, the preparations should be normalized by protein. The dose of 0.6 mg protein per 1 ml solution (12 g protein per kg textile) proves to be suitable when comparing T. reesei preparations and pure enzymes using this method and micromethod B below.

When comparing preparations in one dose, 4 repetitions for each preparation (two vessels with two strips in each) are carried out. It is often more convenient to run a series of 10-16 vessels, with 1 blank (buffer treatment without enzyme) and 1-2 vessels with some standard preparation in each series

Preferably, an alkaline scoured strip should also be added in the heating and evaluation procedure. For alkaline scouring, the strips are treated with a solution of 40 g/l NaOH in a boiling water bath for 2 hours at a liquor ratio of 5-20. Adding surfactant is typically not needed for these samples, but low doses of 1 g/l of EM-3 surfactant or similar products may be beneficial.

The strips can be analyzed without heating after drying overnight. However, heating of the strips provides more reproducible result and leads to a greater difference between well and poorly scoured strips. Drying and conditioning of the strips overnight or longer after heating is an important step and should not be shortened. Results may also be improved by using a special conditioning chamber with constant humidity, rather than leaving the samples at room conditions.

Method B. Micromethod of Scouring and Evaluation Procedure for the Circular Pieces of Textile, Diameter 1.4 cm

Treatment procedure: In this method, circular pieces (diameter 1.4 cm), of the same desized fabric from method A are used. The fabric should be completely wetted in distilled water before the analysis, with excess water removed using filter paper.

A circular piece of textile is placed in a small cylindrical vial (“penicillin vial”, 2.2 cm diameter and 5 cm height) containing 2.0 ml of enzyme solution in 0.1 M Na-acetate buffer (pH 5.0). The vials are placed into a preheated water bath (50° C.) on a shaker (250 rpm) and incubated for 1 hour. The fabric swatch is removed with tweezers, washed 2-3 minutes with cold tap water, and then dried at room temperature conditions overnight. For each enzyme sample and control sample (treatment with no enzyme in buffer), the assay procedure is typically carried out in 2 repetitions (2 pieces).

Heating: Overnight-dried textile swatches are heated for 1 hour at 105° C., then room conditioned overnight prior to being assayed for wettability. Heating generally provides better results, but may be omitted.

Analysis of wettability: Wettability is measured using a drop test. A drop of distilled water, 5 ul, is placed on the surface of fabric and time it takes the drop to adsorb into the material is measured. For each circular piece, 5 measurements are taken, placing each new drop in a dry area within the fabric swatch. The average value for each sample is then calculated.

Enzyme preparations and pure enzymes are tested at 0.6 mg protein per ml solution, but the assays are typically reproducible at doses between 0.6-2.4 mg protein per ml solution This method usually gives greater deviations than method A, but 10-fold less enzyme is needed. Thus, method B is usually recommended where enzyme amounts are limiting.

Testing at one dose with heat treatment reveals preparations of 8-10 cm (e.g. classical ACE, BioACE, IndiAGE 44L, Ecostone L 350, Celloviridin) provide comparative results.

Table 28 and FIG. 20 show the bioscouring ability of cellobiohydrolases and endoglucanases of the present invention. The reciprocal of the time (1/time: sec⁻¹) of water drop adsorption on a textile after treatment at pH 5.0 with 0.6 mg/l of enzyme followed by heating is shown. The water drop adsorption time for the untreated control sample is 2400 sec (l/time=0.0004).

TABLE 28 Bioscouring Abilities of C1 Cellobiohydrolases and Endoglucanases Enzyme 1/Time (sec⁻¹) Blank 0.0004 EG I 0.0006 EG II 0.0006 EG II (CD) 0.0007 EG III 0.0008 EG V 0.0007 EG VI 0.0007 CBH Ia 0.0006 CBH Ia (CD) 0.0006 CBH Ib 0.0006 CBH IIa 0.0006 CBH IIb 0.0006

Qualitative Method for Determination (Staining) of Remaining Pectic Substances in a Scoured Fabric

Ruthenium Red Dye (Sigma, R-2751) is used for specifically staining pectic substances in fabric, by forming a complex with charged carboxyl groups of pectins.

Small swatches (2.5×6 or 2.5×2.5 cm) of scoured fabric are marked using a textile marker. The scoured samples remaining after the wettability analyses described above can be used.

The following controls are included:

1) desized unscoured fabric,

2) control treated with buffer (without an enzyme),

3) alkaline scoured fabric.

All the samples are dyed in one bath and weighed together. The volume of the solution is calculated using the following formula:

V(ml)=m samples (g)×30.

The desired volume of 1 g/l solution of the dye is prepared. The dye solution is stirred and warmed in a boiling water bath for 5 minutes until the dye dissolves completely. The dye solution is warmed in a glass vessel on a water bath shaker set at 50° C., 200 rpm. The samples are then placed in the solution and some surfactant is added if the samples are not wetted. The samples are dyed for 30 minutes at 50° C. with shaking at about 200 rpm for even dying.

Then, the samples are rinsed under tap water followed 3-4 rinses (about 5 minutes each) with hot water (about 70° C. in a glass vessel). After this, the samples are dried overnight at room temperature. The samples should not be iron dried as it may destroy the dye. The samples are generally compared visually, although quantitative colorimetric evaluation can be used.

Example of stained strips are presented in FIG. 21. FIG. 21 illustrates a comparison of the pectin content in an unscoured sample, an alkaline scoured sample, a sample bioscoured by BioPrep (Novo Nordisk, Denmark) at 20 g preparation per 1 kg fabric, and samples bioscoured by ACE at 40 g/kg for 1 or 3 hours.

The unscoured sample and control (treated without enzyme) are stained at high and equal intensity—that means no pectins are removed during buffer treatment. Alkaline scoured sample is very faint stained—100% pectin removed (by definition). All three enzyme scoured samples are also faint, but little bit more intensive than alkaline scoured. This means that cellulase scouring and scouring by BioPrep removes the majority of surface (stainable) pectins from the primary wall, similar to alkaline scouring.

Other positively charged dyes can be used for staining pectins due to the negatively charged polymer in cotton. We have tested methylene blue, but it resulted in less distinction between scoured and unscoured fabric.

Method for Determination of Remaining Waxes in Scoured Textiles

The presence of remaining waxes in scoured textiles is determined using an extraction procedure. 3-12 g of scoured fabric is weighed and then extracted with boiling benzene in a Soxlet apparatus for 4 hours. The extract is evaporated in a rotary evaporator. Then, a flask containing the evaporated, extracted waxes is brought to a constant weight at 105° C. (0.75-1 hour of incubation time is usually necessary). The weight of extracted waxes is then determined and the wax content is calculated.

We compared bioscouring (ACE preparation) and alkaline scouring. Desized cotton strips were treated, dried at room conditions overnight and divided into two parts: one part was evaluated for wicking height, another part were heated to 105° C. for 1 hour, equilibrated at room conditions overnight and then evaluated for wicking height.

Wax content was determined by the method described above, and the results are presented in Table 29 below.

Bioscouring by ACE and by the alkaline procedure gave comparable results based on wicking height changes, but bioscouring removed less wax. Alkaline scouring, however, did not remove all of the wax.

TABLE 29 Bioscouring by ACE versus alkaline scouring. Wicking Wicking height, cm height, cm Type of treatment Room drying heating 105° C., 1 h Waxes, % Untreated cotton 6.0 0 0.62 ± 0.03 Alkaline scouring 13.0 8.4 0.37 ± 0.03 Bioscouring (ACE) 12.4 8.6 0.57 ± 0.03

Example 16

The following example illustrates a method of biopolishing (biofinishing) textiles using enzymes of the present invention.

The method allows for testing small amount of enzymes (mini-testing in the range of 0.5-5 mg of enzyme sample). The method for testing of pure enzymes and crude enzyme preparations is carried out in specially designed cells (essentially a micro-washing machine) also used for the mini-denim washing assay (see FIG. 22B).

Sample preparation: Circular pieces of textile (diameter of 28 mm) are excised from TIC-460 cotton interlock dyed Red 80 fabric. The samples are marked with a textile marker on the side that will be treated with an enzyme and mechanical stress. Each sample is then weighed to an accuracy 1 mg. One piece generally weighs 160 to 180 mg.

Treatment procedure: The sample is fixed in the cell and three metal cylinders are placed into it. When all cells are assembled, 3 ml of enzyme solution are added to each cell. The enzyme solutions contain 0.1 M Na-acetate buffer, pH 5.0, to control the pH. The cells are placed into a preheated Elpan water bath shaker (50° C., 300 rpm, amplitude 4) and the samples are treated for 1 hour.

The efficiency of biopolishing is assayed by measuring the optical density of the reaction solution. Immediately after the treatment, the solution should be thoroughly mixed, using a pipette, to resuspend any possible sediment of removed fuzz. A 1-1.5 ml aliquot of reaction solution is then taken from each cell. The optical density of the solution is then measured on a spectrophotometer at 400 nm in a 1 ml cuvette (1 cm optical path). The solution is resuspended and dosed into the cuvette and the optical density determined rapidly (within 10 seconds), as the suspension sediments gradually and the optical density changes due to sedimentation. If the value of A₄₀₀ exceeds 1 unit, the sample is diluted 2-4 times carefully and the optical density determined once again. If a sample was diluted, the resultant value should be multiplied by the dilution factor.

Rinse and drying: The circular pieces of textile should be rinsed immediately after taking the aliquots of reaction solution, since the enzymatic reaction will proceed otherwise. The sample is removed from the cell, and washed briefly in distilled water. All the samples are then rinsed together thoroughly in distilled water for 3-5 min, stirring gently and changing water periodically. After rinsing, the samples are blotted using filter paper and dried at room temperature for at least 24 hours.

Measurement of the efficiency of biopolishing by determination of the weight loss: Each sample is weighed to a 1 mg accuracy. The resulting values are compared with that of the same sample before the treatment and weight loss is calculated as below:

Weight loss (mg)=m before treatment (mg)−m after treatment (mg)

% Weight loss=Weight loss/m before treatment (mg)×100%

Qualitative evaluation of the surface appearance: The image of the edge of the folded fabric is taken using suitable device at a magnification about ×60. Images of the samples treated by different enzymes and blank runs are compared visually.

In detail, the circular piece is folded (for all samples in a same manner—e.g., so that the surface threads are perpendicular to the edge line). All samples should be folded so that the treated surface is up. The samples can be stapled to a piece of paper for more convenient operation. Images are then taken using a QX3 Intel Play microscope at ×60 magnification and recorded in JPEG format.

The samples should be run in series up to 8 samples in each. In each series, there should be a control treatment (without an enzyme) and a treatment with a standard preparation. For each preparation under investigation, at least 2 repetitions should be made.

Weight determination is influenced by the drying conditions. Drying of the samples before the treatment and after in reproducible conditions is recommended (e.g., heating in an oven and drying in a dessicator). Drying at room conditions can result in slight deviations between series run on different days.

The effect of enzymatic treatment along with mechanical stress in our test is similar to the widely used Launderometer and other laboratory testing machines, but it has different geometry. Due to this geometry, the system is amenable to further miniaturization and require less than 1 mg quantities of an enzyme.

Evaluation of the biopolished fabric can be problematic. The most important (and direct) parameters are pilling resistance and fuzziness of a treated fabric. Weight loss, color clarification, and improvement of softness are less direct but valuable parameters. Greater pilling resistance correlates with greater weight losses and gives less fuzz, clarification of color and softer feel. Fuzziness is evaluated qualitatively in our method on 3 levels: good, moderate and poor. Optical density should correlate directly both to weight loss (weight loss is due mainly to the removed fuzz making turbid suspension in a solution) and fuzziness of fabric.

Table 30 and FIG. 23 illustrate the biopolishing ability of cellobiohydrolases and endoglucanases of the present invention. The dye release (D 400 nm) after treatment with 0.2 g/l enzyme at pH 5.0 and 50° C. is shown.

TABLE 30 Biopolishing Abilities of C1 Cellobiohydrolases and Endoglucanases Enzyme % Dye Release EG I 0.17 EG II 0.2 EG II (CD) 0.1 EG III 0.16 EG V 0.2 EG VI 0.1 CBH Ia 0.1 CBH Ia (CD) 0.2 CBH Ib 0.3 CBH IIa 0.2 CBH IIb 0.1

Example 17

The following example illustrates methods of biostoning (abrasion) textiles using enzymes of the present invention.

The method allow for testing small amount of enzymes (mini-testing in the range of 0.5-5 mg of enzyme sample). The method is available in two scales, requiring approximately 10 and 1 mg of protein, respectively (Method A and Method B). Both scales utilize the same principle and gives comparable results. Method B requires specially designed cells but proved easier when assaying pure enzymes.

Method A

250 ml vessels (internal diameter 56 mm, height 110 mm) with Teflon disks at the bottom (thickness 4 mm) are used for the treatment of denim fabric with cellulase (see FIG. 22A). A swatch of desized denim fabric (10×10 cm) is pulled over the butt of a plastic tube (diameter 50 mm, height 0100 mm) and fixed with a rubber ring. The tube is inserted into the 250 ml vessel so that the swatch attaches tightly and uniformly to the Teflon disk at the bottom of the glass. Ten metal buck-shot balls (diameter 7 mm) are placed inside the tube to provide mechanical stress to the surface of fabric, and 30 ml of enzyme solution in the appropriate buffer is added. The vessel is placed onto a ELPAN water bath shaker type 357 (Poland) at 50° C. The enzymatic treatment of the denim is carried out for 1 hour at the shaker speed of 300 rpm and amplitude of vibrations adjusted to 4 units. The swatch is then removed and washed for 1 minute with running water. An excess of water on the surface of the swatch is removed by squeezing it between two sheets of blotting paper, and then the swatch is dried overnight in the open air at room temperature. In a separate experiment, a control assay is carried out as described above, but in the absence of enzyme. For the control, 30 ml of the same buffer used for enzyme dilution is added to the vessel.

Method B

This assay procedure uses specially designed cylindrical cells (external diameter 35 mm, internal diameter 30 mm, height 48 mm) made of stainless steel and equipped with tightened lids (see FIG. 22B). This method also uses 10-fold less enzyme than Method A. A circular swatch of denim fabric (diameter of 30 mm) is placed at the bottom of a cell, and a stainless steel cylindrical cartridge is inserted to clamp the swatch. Three metal cylinders (7×7 mm), made of stainless steel, are placed into the cell to provide mechanical stress, and 3 ml of enzyme solution in the appropriate buffer is added. A lid, equipped with a rubber ring inside, is quickly tightened to seal the cell hermetically, and the cell is placed in a water bath on a shaker. Then, the procedure is carried under the same conditions as described above for Method A. In the control assay, afacric swatch is treated under the same conditions but in the absence of enzyme. To this end, 3 ml of the same buffer used for enzyme dilution is added to the cell.

Both assays (Method A or Method B) are carried out at least in two repetitions for each particular enzyme (usually three repetitions). Typically, when different cellulase preparations are compared, the conditions in the reaction system are equalized by the CMCase activity (1-3 U/ml). Acid cellulase samples are assayed at pH 5.0 using 0.1 M acetate buffer. Neutral cellulases are assayed at pH 6.0 using 0.1 M phosphate buffer.

Analysis of color intensity on denim swatches is carried out using a Mustek MFS-12000SP (USA) scanner. A circular area on the swatch, subjected to the combined enzyme and mechanical action as above, is scanned at 300 dpi resolution. This area is usually more light than the denim surface near the swatch edges. Each swatch is scanned twice: first, when the threads on the surface of the fabric are parallel to the movement of the light source on scanning, and second, when the threads are directed perpendicular to the movement of the light source on scanning.

The JPG images obtained as a result of scanning are analyzed using Adobe Photoshop software (versions 3.0 or later can be used). For each particular scan, a histogram is opened. The blue channel is selected and the percentile at level 32 (P32) is read. This parameter shows the percentage of image pixels having the intensity of color higher than at the level 32 of histogram (a total of 256 shades (levels) of blue color as the abscissa axis). The higher is the P32, the darker is the denim swatch. On the contrary, the parameter (100—P32, %) shows the percentage of pixels having the intensity of color lower than at the level 32 of the histogram. FIG. 24 shows an example histogram generated from the color intensity analysis of a denim swatch.

For each particular enzyme tested, an average value of the P32 and standard deviation are calculated using the data of all scans for this enzyme. For example, if the assay is performed in two repetitions, four P32 values are taken into account, since for each repetition two scans are carried out.

The difference between the average value of P32 obtained in the control (without cellulase) and the average value of P32 for the enzyme is taken as a criterion of the abrasive activity of the enzyme.

Table 31 and FIG. 25 illustrate the denim-washing (abrasion) ability of cellobiohydrolases and endoglucanases of the present invention using Assay B above. The relative units per mg of enzyme determined at 50° C., pH 5.0 is shown.

TABLE 31 Abrasion Abilities of C1 Cellobiohydrolases and Endoglucanases Enzyme Relative Units per mg EG I 14 EG II 62 EG II (CD) 54 EG III 25 EG V 65 EG VI 12 CBH Ia 3 CBH Ia (CD) 11 CBH Ib 10 CBH IIa 22 CBH IIb. 15

Additional examples and discussion concerning methods A and B are presented in A. Gusakov, A. Smitsyn, S. Grishutin, D. Tikhomirov, D. Shook, D. Sheer, M. Emalfarb Microassays to control the results of cellulase treatment of denim fabrics; Textile Chemist and Colorist and American Dyestuff Reporter, (2000), V.32, N. 5, P. 42, the contents of which are hereby incorporated by reference in their entirety.

Example 18

The following example illustrates methods of backstaining textiles using enzymes of the present invention.

The methods allow for testing small amount of enzymes (mini-testing in the range of 0.5-5 mg of enzyme sample).

Standard Indigo backstaining Method A requires larger enzyme quantities (typically 2-5 mg of protein for one assay performed with 3.5×3.5 cm swatches in 2-3 repetitions). When purification of enzyme components is performed on a laboratory scale and it is necessary to assay the backstaining index (BSI) for the purified enzyme, much lower quantities of an enzyme are typically available. In such case, a modification of this method (Method B) should be used, where smaller swatches of standard garment (1.4×1.4 cm) are used, and the total volume of Indigo suspension is 2 ml. This minimized microassay procedure requires ten times lower amounts of protein (0.2-0.5 mg).

Method A

Indigo reagent preparation: 250 mg of indigo is added to 50 ml of distilled water in a flask and stirred vigorously for 15-20 minutes on a magnetic stirrer. Before taking aliquots for staining experiments, the suspension is placed into a Bandelin SONOREX TK52 ultrasonic bath for 5 minutes to disrupt large indigo aggregates and to make the suspension more uniform.

2 ml aliquots are used for staining experiments (see below) under magnetic stirring in order to provide a uniform indigo suspension in the reaction mixture.

Assay procedure: A piece of white fabric (3.5×3.5 cm) is added to 18 ml of 0.1 M Na-acetate buffer (pH 5.0) in a 250 ml glass vessel and incubated at room temperature for 10 minutes (control). A solution of enzyme preparation in the same amount of the buffer is used in the enzyme assay procedure. 2 ml of indigo suspension (5 mg/ml) is then added, and the vessel is placed into a water bath (50° C.) on a shaker (300 rpm) and agitated for 30 min. The piece of fabric is removed with tweezers and washed twice for 5 minutes with 50 ml of distilled water (on a shaker at 300 rpm) and then dried at room temperature overnight. For each enzyme sample and control, the assay procedure is carried out at least in 3 repetitions.

Samples of stained fabric are scanned at 300 dpi resolution on a “Paragon” (“Murtek”, USA) scanner. Two images of the front side and two images of the back side (one direct and one rotated 90°) are obtained for each sample. Images are processed using an Adobe Photoshop software. A histogram of colour intensities is calculated for each sample using a blue channel, and a percentile at level 120 is used as a criterion of staining. An average value and standard deviation are calculated for each enzyme preparation and control.

T. reesei (ACE) is usually used as a control (internal standard) for analyzing backstaining properties of a particular enzyme sample, since ACE is characterized by a high backstaining index. If possible, a IndiAge Super GX sample should be used as a second internal standard since it has a low backstaining index.

Method B

The Indigo stock suspension (5 g/l) is prepared and the image processing is carried out as described above.

Assay procedure: A piece of white fabric (1.4×1.4 cm) is placed in a small cylindrical vial (“penicllin vial”, 2.2 cm diameter and 5 cm height) containing 1.8 ml of enzyme solution in 0.1 M Na-acetate buffer (pH 5.0) and incubated at room temperature for 10 min. 0.2 ml of Indigo suspension is then added, and the vial is placed into a water bath (50° C.) on a shaker (300 rpm) and agitated for 30 minutes. The fabric swatch is removed with tweezers and washed twice for 5 minutes with 5 ml of distilled water at 50° C. (on a shaker at 300 rpm), then dried at room temperature overnight. For each enzyme sample and control (internal standard), the assay procedure is typically carried out in 3 repetitions. In most experiments, 1.5 CMCase units per ml of reaction system are used. In cases where specific CMCase activity is very low (or absent), 0.05-0.1 mg of protein per ml of reaction system is used.

It is convenient to place three vials (3 repetitions) into a 250 ml vessel containing 15-20 ml of water at the bottom and then to place the vessel into a water bath on a shaker.

Additional examples and discussion concerning methods A and B are presented in A. Gusakov, A. Sinitsyn, S. Grishutin, D. Tikhomirov, D. Shook, D. Sheer, M. Emalfarb Microassays to control the results of cellulase treatment of denim fabrics; Textile Chemist and Colorist and American Dyestuff Reporter, (2000), V.32, N. 5, P. 42, the contents of which are hereby incorporated by reference in their entirety.

Example 19

The following example illustrates assays used to measure acetyl esterase enzymatic activity.

Activity Towards p-Nitrophenyl Acetate Substrate

This assay measures the release of p-nitrophenol by the action of an acetyl esterase on p-nitrophenyl acetate (PNPAc). One acetyl esterase unit of activity is the amount of enzyme that liberates 1 micromole of p-nitrophenol in one minute at 37° C. and pH 7.2.

Phosphate buffer (0.01 M, pH 7.2) is prepared as follows: 0.124 g of NaH₂PO₄*H₂O and 0.178 g NaMPO₄ are dissolved in distilled water so that the final volume of the solution 500 ml and the pH of the resulting solution is 7.2.

PNPAc (Fluka Chemie, Switzerland, cat. #46021) is used as the assay substrate. 3.6 mg of PNPAc is dissolved in 10 ml of 0.01 M phosphate buffer using a magnetic stirrer to obtain a 2 mM stock solution. The solution is stable for 2 days with storage at 4° C.

The stop reagent (0.25 M Tris-HCl, pH 8.5) is prepared as follows: 30.29 g of Tris is dissolved in 900 ml of distilled water (Solution A). The final 0.25 M Tris-HCl pH 8.5 is prepared by mixing solution A with 37% HCl until the pH of the resulting solution is equal to 8.5. The solution volume is then adjusted to 1000 ml. This reagent is used to terminate the enzymatic reaction. Using the above reagents, the assay is performed as detailed below.

For the enzyme sample, 0.10 ml of 2 mM PNPAc stock solution is mixed with 0.01 ml of an enzyme sample and incubated at 37° C. for 5 minutes (Axe2 and Axe3) or 10 minutes (Axe1). After exactly 5 or 10 minutes of incubation, 0.1 ml of 0.25 M Tris-HCl solution is added and then the absorbance at 405 nm (A₄₀₅) is measured in microtiter plates as A_(S).

For the substrate blank, 0.10 mL of 2 mM PNPAc stock solution is mixed with 0.01 ml of 0.01 M phosphate buffer, pH 7.2. 0.1 mL of 0.25 M Tris-HCl solution is then added and the absorbance at 405 nm (A₄₀₅) is measured in microtiter plates as A_(SB).

Activity is calculated as follows:

${{Activity}\mspace{14mu} \left( {I\; U\text{/}{ml}} \right)} = \frac{\Delta \; A_{405}*{DF}*21*1.33}{13.700*5}$

where ΔA₄₀₅=A_(S)−A_(SB), DF is the enzyme dilution factor, 21 is the dilution of 10 μl enzyme solution in 210 μl reaction volume, 1.33 is the conversion factor of microtiter plates to cuvettes, 13.700 is the extinction coefficient (13700 M⁻¹ cm⁻¹ of p-nitrophenol released corrected for mol/L to mmol/mL), and 5 minutes is the reaction time.

Using the assay above, acetyl esterase activity of Axe1 was found to be 0.23 IU/mL (ΔA₄₀₅=1.11, DF=1), Axe2 was found to be 2.80 U/ml (ΔA₄₀₅=0.1714, DF=40), and Axe3 was found to be 39.97 U/ml (ΔA₄₀₅=0.4901, DF=200).

Activity Towards Arabinoxylan Oligosaccharide Substrates

This assay measures the release of acetate by the action of a xylan acetyl esterase on the arabinoxylan oligosaccharides from Eucalyptus wood.

0.01 M sodium hydroxide is prepared as follows: 0.4 g of sodium hydroxide is dissolved in distilled water so that the final volume of the solution to be 1000 ml

Arabinoxylan oligosaccharides from Eucalyptus wood were prepared by dissolving 5 me of arabinoxylan oligosaccharides in 1 ml distilled water using a magnetic stirrer as described in Kabel et al. Carbohdr. Polym. 50:191 (2002).

For the enzyme sample, 1.0 mL of arabinoxylan oligosaccharides stock solution is mixed with 0.005 mg of the enzyme sample and incubated at 35° C. The pH was maintained at 5.0 by the addition of 0.01 M NaOH. The added volume of 0.01 M NaOH is proportional to the breakdown of ester linkage and release of acetate.

For the substrate blank, 1.0 ml of arabinoxylan oligosaccharides stock solution is mixed with 0.005 mg of distilled water and incubated at 35° C. The pH was maintained at 5.0 by addition of 0.01 M NaOH. The added volume of 0.01 M NaOH is proportional to the breakdown of ester linkage and release of acetate.

Using the assay above, both Axe2 and Axe3 were found to exhibit xylan acetyl esterase activity, as measured by the release of acetate from eucalyptus wood arabinoxylan oligosaccharides. For Axe2, 0.7 ml NaOH was used after 200 minutes of incubation. For Axe3, 0.35 ml was used after 200 minutes.

Example 20

The following example illustrates assays used to measure ferulic acid esterase enzymatic activity.

Activity towards p-Nitrophenyl Butyrate Substrate

This assay measures the release of p-nitrophenol by the action of a ferulic acid esterase on p-nitrophenyl butyrate (PNPBu). One acetyl esterase unit of activity is the amount of enzyme that liberates 1 micromole of p-nitrophenol in one minute at 37° C. and pH 7.2.

Phosphate buffer (0.01 M, pH 7.2) is prepared as follows: 0.124 g of NaH₂PO₄*H₂O and 0.178 g Na₂HPO₄ are dissolved in distilled water so that the final volume of the solution is 500 ml and the pH of the resulting solution is equal to 7.2.

PNPBu (Sigma, USA, cat. #N9876-5G) is used as the assay substrate. 10 μl of PNPBu is mixed with 25 ml of 0.01 M phosphate buffer using a magnetic stirrer to obtain a 2 mM stock solution. The solution is stable for 2 days with storage at 4° C.

The stop reagent (0.25 M Tris-HCl, pH 8.5) is prepared as follows: 30.29 g of Tris is dissolved in 900 ml of distilled water (Solution A). The final 0.25 M Tris-HCl pH 8.5 is prepared by mixing solution A with 37% HCl until the pH of the resulting solution is equal to 8.5. The solution volume is adjusted to 1000 ml. This reagent is used to terminate the enzymatic reaction. Using the above reagents, the assay is performed as detailed below.

For the enzyme sample, 0.10 ml of 2 mM PNPBu stock solution is mixed with 0.01 ml of the enzyme sample and incubated at 37° C. for 10 minutes. After exactly 10 minutes of incubation, 0.1 ml of 0.25 M Tris-HCl solution is added and then the absorbance at 405 nm (A₄₀₅) is measured in microtiter plates as A_(S).

For the substrate blank, 0.10 ml of 2 mM PNPBu stock solution is mixed with 0.01 ml of 0.01 M phosphate buffer, pH 7.2. 0.1 ml of 0.25 M Tris-HCl solution is then added and the absorbance at 405 nm (A₄₀₅) is measured microtiter plates as A_(SB).

Activity is calculated as follows:

${{Activity}\mspace{14mu} \left( {I\; U\text{/}{ml}} \right)} = \frac{\Delta \; A_{405}*{DF}*21*1.33}{13.700*10}$

where ΔA₄₀₅=A_(S)−A_(SB), DF is the enzyme dilution factor, 21 is the dilution of 10 μl enzyme solution in 210 μl reaction volume, 1.33 is the conversion factor of microtiter plates to cuvettes, 13.700 is the extinction coefficient (13700 M⁻¹ cm⁻¹ of p-nitrophenol released corrected for mol/l to μmol/ml), and 10 minutes is the reaction time.

Using the assay above, the ferulic acid esterase activity of FaeA1 was found to be 18.5 IU/ml (ΔA₄₀₅=0.906, DF=10), FaeA2 was found to be 0.40 U/ml (ΔA₄₀₅=1.976, DF=1) and FaeB2 was found to be 0.02 U/ml (ΔA₄₀₅=0.111, DF=1).

Activity Towards p-Nitrophenyl Butyrate Substrate

The following assay is used to measure the enzymatic activity of a ferulic acid esterase towards wheat bran (WB) oligosaccharides by measuring the release of ferulic acid.

Wheat bran oligosaccharides are prepared by degradation of wheat bran (obtained from Nedalco, The Netherlands) by endo-xylanase III from A. niger (enzyme collection Laboratory of Food Chemistry, Wageningen University, The Netherlands). 50 mg of WB is dissolved in 10 ml of 0.05 M acetate buffer pH 5.0 using a magnetic stirrer. 1.0 ml of WB stock solution is mixed with 0.0075 mg of the enzyme and incubated at 35° C. for 24 hours. The reaction is stopped by heating the samples for 10 minutes at 100° C. The residual material is removed by centrifugation (15 minutes at 14000 rpm), and the supernatant is used as the substrate in the assay detailed below.

For the enzyme sample, 1.0 ml of wheat bran oligosaccharides stock solution is mixed with 0.005 mg of the enzyme sample and incubated at 35° C. for 24 hours. The reaction is stopped by heating the samples for 10′ minutes at 100° C. The release of ferulic acid is analyzed by measuring the absorbance at 335 nm.

For the substrate blank, 1.0 ml of wheat bran oligosaccharides stock solution is mixed with 0.005 mg of 0.05 M acetate buffer, pH 5.0, and incubated at 35° C. for 24 hours. The reaction is stopped by heating the samples for 10 minutes at 100° C. The release of ferulic acid is analyzed by measuring the absorbance at 335 nm.

Using the assay above, FaeA1 was found to release ferulic acid from wheat bran arabinoxylan oligosaccharides, releasing 75% of the ferulic acid present in wheat bran. FaeA1 also exhibited activity towards sugar beet pulp oligosaccharides (20% hydrolysis). FaeB2 was found to release 80% of the ferulic acid present in wheat bran. FaeB2 also exhibited activity towards sugar beet pulp oligosaccharides (16% hydrolysis).

Example 21

The following example illustrates an assay used to measure α-arabinofuranosidase enzymatic activity.

This assay measures the release of arabinose by the action of the α-arabinofuranosidase on wheat arabinoxylan oligosaccharides (WAX).

Acetate buffer (0.05 M, pH 5.0) is prepared as follows: 4.1 g of anhydrous sodium acetate or 6.8 g of sodium acetate*3H₂O is dissolved in distilled water so that the final volume of the solution to be 1000 ml (Solution A). In a separate flask, 3.0 g (2.86 mL) of glacial acetic acid is mixed with distilled water to make the total volume 1000 ml (Solution B). The final 0.05 M acetate buffer, pH 5.0, is prepared by mixing Solution A with Solution B until the pH of the resulting solution is equal to 5.0.

Wheat arabinoxylan oligosaccharides are prepared by degradation of Wheat arabinoxylan (Megazyme, Bray Ireland, Cat. #P-WAXYI) by endo-xylanase I from A. niger (enzyme collection Laboratory of Food Chemistry, Wageningen University, The Netherlands). 50 mg of WAX is dissolved in 10 ml 0.05 M acetate buffer, pH 5.0, using a magnetic stirrer. 1.0 ml of WAX stock solution is mixed with 0.0075 mg of the enzyme and incubated at 35° C. for 24 hours. The reaction is stopped by heating the samples for 10 minutes at 100° C. The residual material is removed by centrifugation (15 minutes at 14000 rpm), and the supernatant is used as the substrate in the assay detailed below.

For the enzyme sample, 1.0 ml of wheat arabinoxylan oligosaccharides stock solution is mixed with 0.0075 mg of the enzyme sample and incubated at 35° C. for 24 hours. The reaction is stopped by heating the samples for 10 minutes at 100° C. The release of arabinose and formation of new arabinoxylan oligosaccharides were analyzed by High Performance Anion Exchange Chromatography.

For the substrate blank, 1.0 ml of wheat arabinoxylan oligosaccharides stock solution is mixed with 0.0075 mg of the 0.05 M acetate buffer, pH 5.0, and incubated at 35° C. for 24 hours. The reaction is stopped by heating the samples for 10 minutes at 100° C. The release of arabinose and formation of new arabinoxylan oligosaccharides were analyzed by High Performance Anion Exchange Chromatography.

High Performance Anion Exchange Chromatography analysis is performed using a Dionex HPLC system equipped with a Dionex CarboPac PA-1 (2 mm ID×250 mm) column in combination with a CarboPac PA guard column (1 mm ID×25 mm) and a Dionex EDet1 PAD-detector (Dionex Co., Sunnyvale, Calif., USA). A flow rate of 0.3 ml/min was used with the following gradient of sodium acetate in 0.1 M NaOH: 0-5 min, 0-100 mM; 5-45 min. 100-400 mM. Each elution was followed by a washing step of 5 minutes 1,000 mM sodium acetate in 0.1 M NaOH and an equilibration step of 15 minutes 0.1 M NaOH.

Using the above assay, both Abf1 and Abf2 were found to release arabinose from wheat arabinoxylan oligosaccharides. Both enzymes removed arabinose residues, which were monosubstituted to the xylose backbone. Arabinose residues linked to O2 and O3 position of the xylose residue were released by both Abf1 and Abf2.

Example 22

The following example illustrates an assay used to measure pectin methyl esterase enzymatic activity.

The following assay is used to measure the enzymatic activity of a pectin methyl esterase towards highly methylated citrus pectin (DM 65) in combination with methyl red. The assay measures the release of methanol by the action of pectin methyl esterases on methylated citrus pectin. The release of methanol will acidify a solution (non-esterified galacturonic acid), which makes the methyl red indicator change color at a pH of less than 4.4.

Pectin-methyl red solution is prepared as follows: 0.5 g of methylated citrus pectin (DM 65, Sigma, USA, Cat. #P9436-5G). 2 mg methyl red (Sigma, USA) and 0.435 g NaCl is dissolved in distilled water so that the final volume of the solution is 50 ml. The final pH is adjusted to 5.0 by adding 0.1 M NaOH.

For the enzyme sample, 0.1 ml of pectin-methyl red stock solution is mixed with 0.01 ml of the enzyme sample and incubated at 37° C. overnight. The absorbance at 520 nm. (A₅₂₀) is measured as A_(S).

For the substrate blank, 0.1 ml of pectin/methyl red stock solution is mixed with 0.01 ml of distilled water and incubated at 37° C. overnight. The absorbance at 520 nm (A₅₂₀) is measured as A_(SB).

Using the assay above, the ΔA₅₂₀ of Pme1 was found to be 0.401, demonstrating that Pme1 is active towards highly methylated pectin.

Example 23

The following example illustrates an assay used to measure endo-arabinase enzymatic activity.

The assay is used to measure the enzymatic activity of an endo-arabinase towards AZCL-arabinan (debranched). This substrate is insoluble in buffered solutions, but rapidly hydrates to form gel particles that are hydrolysed by specific endo-hydrolases, releasing soluble dye-labeled fragments.

Acetate buffer (0.05 M, pH 5.0) is prepared as follows: 4.1 g of anhydrous sodium acetate or 6.8 g of sodium acetate*3H₂O is dissolved in distilled water so that the final volume of the solution is 1000 ml (Solution A). In a separate flask, 3.0 g (2.86 ml) of glacial acetic acid is mixed with distilled water to yield a total volume of 1000 ml (Solution B). The final 0.05 M acetate buffer, pH 5.0, is prepared by mixing Solution A with Solution B until the pH of the resulting solution is equal to 5.0.

AZCL-arabinan (debranched) from Megazyme (Bray, Ireland, Cat. #I-AZDAR) is used as the assay substrate. 50 mg of AZCL-arabinan is dissolved in 10 ml of 0.05 M acetate buffer, pH 5.0, using a magnetic stirrer. 96% Ethanol is used to terminate the enzymatic reaction.

For the enzyme sample, 0.2 ml of 5 mg/ml AZCL-arabinan stock solution is preheated to 40° C. for 1.0 minutes. This preheated stock solution is mixed with 200 μl of the enzyme sample (preheated at 40° C. for 10 minutes) and incubated at 40° C. for 10 minutes. After exactly 10 minutes of incubation, 1.0 ml of 96% ethanol is added and the absorbance at 590 nm (A₅₉₀) is then measured as A_(S).

For the substrate blank, 1.2 ml of 5 mg/ml AZCL-arabinan stock solution is preheated at 40° C. for 10 minutes. This preheated stock solution is mixed with 200 μl of 0.05 M acetate buffer pH 5.0 (preheated at 40° C. for 10 minutes) and incubated at 40° C. for 10 minutes. After exactly 10 minutes of incubation, 1.0 ml of 96% ethanol is added and the absorbance at 590 nm (A₅₉₀) is then measured as A_(SB).

Endo-arabinase activity is determined using a standard curve produced from an endo-arabinase with known activity towards AZCL-arabinan. Activity (IU/ml)=ΔA₅₉₅*DF, where ΔA₅₉₅=A_(S)−A_(SB) and DF is the enzyme dilution factor.

Using the above assay, the ΔA₅₉₅ was found to be 1.53 with a DF of 1, indicating that Abn1 exhibits endo-arabinase activity towards AZCL-arabinan.

Example 24

The following example illustrates an assay used to measure β-xylosidase enzymatic activity.

This assay measures the release of p-nitrophenol by the action of a β-xylosidase on p-nitrophenyl β-D-xylopyranoside (PNPX). One β-xylosidase unit of activity is the amount of enzyme that liberates 1 micromole of p-nitrophenol in one minute at 37° C. and pH 5.0.

Acetate buffer (0.1 M, pH 5.0) is prepared as follows: 8.2 g of anhydrous sodium acetate or 13.6 g of sodium acetate*3H₂O is dissolved in distilled water so that the final volume of the solution is 1000 ml (Solution A). In a separate flask, 6.0 g (5.72 ml) of glacial acetic acid is mixed with distilled water to make the total volume of 1000 ml (Solution B). The final 0.1 M acetate buffer, pH 5.0, is prepared by mixing Solution A with Solution B until the pH of the resulting solution is equal to 5.0.

PNPX (Extrasynthese, France, Cat. #4244) is used as the assay substrate. 16.5 mg of PNPX is dissolved in 5 ml of distilled water and 5 ml 0.1 M acetate buffer using a magnetic stirrer to obtain 2 mM stock solution. The solution is stable for 2 days with storage at 4° C.

The stop reagent (0.25 M sodium carbonate solution) is prepared as follows: 26.5 g of anhydrous sodium carbonate is dissolved in 800 ml of distilled water, and the solution volume is adjusted to 1000 ml. This reagent is used to terminate the enzymatic reaction.

For the enzyme sample, 0.10 ml of 2 mM PNPX stock solution is mixed with 0.01 ml of the enzyme sample and incubated at 37° C. for 30 minutes. After exactly 30 minutes of incubation, 0.1 ml of 0.25 M sodium carbonate solution is added and the absorbance at 405 nm (A₄₀₅) is then measured in microtiter plates as A_(S).

For the substrate blank, 0.10 ml of 2 mM PNPX stock solution is mixed with 0.01 ml of 0.05 M acetate buffer, pH 5.0. 0.1 mL of 0.25 M sodium carbonate solution is then added and the absorbance at 405 nm (A₄₀₅) is measured microtiter plates as A_(SB).

Activity is calculated as follows:

${{Activity}\mspace{14mu} \left( {I\; U\text{/}{ml}} \right)} = \frac{\Delta \; A_{405}*{DF}*21*1.33}{13.700*30}$

where ΔA₄₀₅=A_(S)−A_(SB), DF is the enzyme dilution factor, 21 is the dilution of 10 μl enzyme solution in 210 μl reaction volume, 1.33 is the conversion factor of microtiter plates to cuvettes, 13.700 is the extinction coefficient 13700 M cm⁻¹ of p-nitrophenol released corrected for mol/l to μmol/ml, and 30 minutes is the reaction time.

Using the above assay, Bxl2 was found to exhibit a β-xylosidase activity of 0.09 IU/ml (ΔA₄₀₅=1.36, DF=1).

Example 25

The following example illustrates an assay used to measure the saccharification ability of enzymes of the present invention.

The hydrolysis of 5 g/l Avicel catalyzed by purified cellulases was performed for 120 hours at 40° C. and pH 5.0. Avicel substrate (10 mg) was mixed with 1.0 ml of 0.1 M Na-acetate buffer, pH 5.0, containing 1 mM of sodium azide to prevent microbial growth, in a 2 ml vial. The vial was incubated in a thermostatic water bath equipped with a magnetic stirrer. The enzyme solution (1 ml), diluted as needed to reach a particular concentration, was added and the mixture was stirred. Equal protein concentrations (0.1 mg/ml) were used for all enzyme preparations. To convert cellooligosaccharides, which are soluble products of cellulose hydrolysis catalyzed by endoglucanases and cellobiohydrolases, into a final hydrolysis product (glucose) and thus simplify the analysis of hydrolyzate, highly purified beta-glucosidase from A. japonicus (0.2 U/ml; see below) was added to the reaction mixture. Aliquots of the suspension (0.1 ml) were collected from the reaction mixture and centrifuged after fixed time intervals. Glucose concentration in the supernatant was determined by the glucose oxidase-peroxidase method (see Example 6).

Beta-glucosidase was purified from A. japonicus culture filtrates using anion-exchange chromatography on SOURCE Q media (pH 5.5, gradient of NaCl; GE Healthcare, USA) followed by hydrophobic chromatography on Phenyl SUPEROSE media (GE Healthcare, USA) in a gradient of ammonium sulfate.

Table 32 and FIG. 26 show a graph of the saccharification ability of cellobiohydrolases and endoglucanases of the present invention. The amount of glucose (g/l) produced after the hydrolysis of 5 g/l Avicel at pH 5.0, 40° C. for 120 hours in the presence of 0.1 mg/ml enzyme and 0.2 U/ml beta-glucosidase is shown.

TABLE 32 Saccharification Abilities of C1 Cellobiohydrolases and Endoglucanases Enzyme Glucose Yield (g/l) EG I 1.2 EG II 0.97 EG II (CD) 0.4 EG III 0.42 EG V 0.51 EG VI 0.56 CBH Ia 2.54 CBH Ia (CD) 1.31 CBH Ib 1.25 CBH IIa 1.16 CBH IIb 3.2

While various embodiments of the present invention have been described in detail, it is apparent that modifications and adaptations of those embodiments will occur to those skilled in the art. It is to be expressly understood, however, that such modifications and adaptations are within the scope of the present invention, as set forth in the following claims. 

1. An isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of: a) a nucleic acid sequence encoding a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:11, SEQ ID NO:23, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38, SEQ ID NO:41, SEQ ID NO:44, SEQ ID NO:50, SEQ ID NO:53, SEQ ID NO:56, SEQ ID NO:59, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77, SEQ ID NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, SEQ ID NO:92, and SEQ ID NO:94, b) a nucleic acid sequence encoding a fragment of the protein of (a), wherein the fragment has a biological activity of the protein of (a); and c) a nucleic acid sequence encoding an amino acid sequence that is at least 70% identical to an amino acid sequence of (a) and has a biological activity of the protein comprising the amino acid sequence.
 2. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence encodes an amino acid sequence that is at least 90% identical to the amino acid sequence of (a) and has a biological activity of the protein comprising the amino acid sequence.
 3. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence encodes an amino acid sequence that is at least 95% identical to the amino acid sequence of (a) and has a biological activity of the protein comprising the amino acid sequence.
 4. The isolated nucleic acid molecule of claim 0, wherein said nucleic acid sequence encodes an amino acid sequence that is at least 97% identical to the amino acid sequence of (a) and has a biological activity of the protein comprising the amino acid sequence.
 5. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence encodes an amino acid sequence that is at least 99% identical to the amino acid sequence of (a) and has a biological activity of the protein comprising the amino acid sequence.
 6. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:11, SEQ ID NO:23, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38, SEQ ID SEQ ID NO:44, SEQ ID NO:50, SEQ ID NO:53, SEQ ID NO:56, SEQ ID NO:59, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77, SEQ ID NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, SEQ ID NO:92, and SEQ ID NO:94.
 7. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence consists of a nucleic acid sequence selected from the group consisting of: SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:52, —SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:78, SEQ ED NO:79, SEQ ID NO:90, SEQ ID NO:91 and SEQ ID NO:93.
 8. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence of (a) encodes a protein comprising the amino acid sequence of SEQ ID NO:11, wherein the protein has cellobiohydrolase activity.
 9. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence of (a) encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:94 and SEQ ID NO:23, wherein the protein has endoglucanase activity.
 10. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence of (a) encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38 and SEQ ID NO:41, wherein the protein has xylanase activity.
 11. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence of (a) encodes a protein comprising an amino acid sequence of SEQ ID NO:44, wherein the protein has β-glucosidase activity.
 12. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence of (a) encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:50, SEQ ID NO:53, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77, SEQ ID NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, and SEQ ID NO:92, wherein the protein has hemicellulase activity.
 13. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence of (a) encodes a protein comprising the amino acid sequence of SEQ ID NO:50, wherein the protein has glucoamylase activity.
 14. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence of (a) encodes a protein comprising the amino acid sequence of SEQ ID NO:53, wherein the protein has pectate lyase activity.
 15. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence of (a) encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:56 and SEQ ID NO:59, wherein the protein has chitinase activity.
 16. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence of (a) encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:62, SEQ ID NO:80, and SEQ ID NO:83, wherein the protein has acetylxylan esterase activity.
 17. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence of (a) encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:65, SEQ ID NO:68, and SEQ ID NO:71, wherein the protein has ferulic acid esterase activity.
 18. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence of (a) encodes a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:74 and SEQ ID NO:77, wherein the protein has arabinofuranosidase activity.
 19. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence of (a) encodes a protein comprising the amino acid sequence of SEQ ID NO:86, wherein the protein has pectin methyl esterase activity.
 20. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence of (a) encodes a protein comprising the amino acid sequence of SEQ ID NO:89, wherein the protein has endo-arabinase activity.
 21. The isolated nucleic acid molecule of claim 1, wherein said nucleic acid sequence of (a) encodes a protein comprising the amino acid sequence of SEQ ID NO:92, wherein the protein has β-xylosidase or β-glucosidase activity.
 22. An isolated nucleic acid molecule comprising a nucleic acid sequence encoding a protein comprising an amino acid sequence selected from the group consisting of: SEQ ID NO:2 and SEQ ID NO:5.
 23. An isolated nucleic acid molecule comprising a nucleic acid sequence that is fully complementary to the nucleic acid sequence of the nucleic acid molecule of any one of claims 1 to
 22. 24. An isolated protein comprising an amino acid sequence encoded by the nucleic acid molecule of any one of claims 1 to
 22. 25. An isolated protein comprising an amino acid sequence encoded by the nucleic acid molecule of claim
 15. 26. An isolated fusion protein comprising the isolated protein of claim 24 fused to a protein comprising an amino acid sequence that is heterologous to the isolated protein of claim
 24. 27. An isolated antibody or antigen binding, fragment thereof that selectively binds to the protein of claim
 24. 28. A kit for degrading a lignocellulosic material to fermentable sugars comprising at least one isolated protein of claim
 24. 29. A detergent comprising at least one isolated protein of claim
 24. 30. A composition for the degradation of a lignocellulosic material comprising at least one isolated protein of claim
 24. 31. A recombinant nucleic acid molecule comprising the isolated nucleic acid molecule of any one of claims 1 to 22, operatively linked to at least one expression control sequence.
 32. The recombinant nucleic acid molecule of claim 31, wherein the recombinant nucleic acid molecule comprises an expression vector.
 33. The recombinant nucleic acid molecule of claim 31, wherein the recombinant nucleic acid molecule comprises a targeting vector.
 34. An isolated host cell transfected with the nucleic acid molecule of any one of claims 1 to
 22. 35. The isolated host cell of claim 34, wherein the host cell is a fungus.
 36. The isolated host cell of claim 34, wherein the host cell is a filamentous fungus.
 37. The isolated host cell of claim 36, wherein the filamentous fungus is from a genus selected from the group consisting of: Chrysosporium, Thielavia, Neurospora, Aureobasidium, Filibasidium, Piromyces, Corynascus, Cryplococcus, Acremonium, Tolypocladium, Scytalidium, Schizophyllum, Sporotrichum, Penicillium, Gibberella, Myceliophthora, Mucor, Aspergillus, Fusarium, Humicola, and Trichoderma, and anamorphs and teleomorphs thereof.
 38. The isolated host cell of claim 34, wherein the host cell is a bacterium.
 39. An oligonucleotide consisting essentially of at least 12 consecutive nucleotides of a nucleic acid sequence selected from the group consisting of: SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:79, SEQ ID NO:90, SEQ ED NO:91, and SEQ ID NO:93, or the complement thereof.
 40. A kit comprising at least one oligonucleotide of claim
 39. 41. A method for producing the protein of claim 24, comprising culturing a cell that has been transfected with a nucleic acid molecule comprising a nucleic acid sequence encoding the protein, and expressing the protein with the transfected cell.
 42. The method of claim 41, further comprising recovering the protein from the cell or from a culture comprising the cell.
 43. A genetically modified organism comprising components suitable for degrading a lignocellulosic material to fermentable sugars, wherein the organism has been genetically modified to express at least one protein of claim
 24. 44. The genetically modified organism of claim 43, wherein the genetically modified organism is a microorganism.
 45. The genetically modified organism of claim 44, wherein the microorganism is a filamentous fungus.
 46. The genetically modified organism of claim 45, wherein the filamentous fungus is from a genus selected from the group consisting of: Chrysosporium, Thielavia, Neurospora, Aureobasidium, Filibasidium, Piromyces, Corynascus, Cryplococcus, Acremonium, Tolypocladium, Scytalidium, Schizophyllum, Sporotrichum, Penicillium, Talaromyces, Gibberella, Myceliophthora, Mucor, Aspergillus, Fusarium, Humicola, and Trichoderma.
 47. The genetically modified organism of claim 45, wherein the filamentous fungus is selected from the group consisting of: Trichoderma reesei, Chrysosporium lucknowense, Aspergillus japonicus, Penicillium canescens, Penicillium solitum, Penicillium funiculosum, and Talaromyces flavus.
 48. The genetically modified organism of claim 43, wherein the organism has been genetically modified to express at least one additional enzyme.
 49. The genetically modified organism of claim 48, wherein the additional enzyme is an accessory enzyme selected from the group consisting of: cellulase, xylanase, ligninase, glucuronidase, arabinofuranosidase, arabinogalactanase, ferulic acid esterase, lipase, pectinase, glucomannase, amylase, laminarinase, xyloglucanase, galactanase, glucoamylase, pectate lyase, chitinase, exo-•-D-glucosaminidase, cellobiose dehydrogenase, and acetylxylan esterase.
 50. The genetically modified organism of claim 43, wherein the genetically modified organism is a plant.
 51. A recombinant enzyme isolated from the genetically modified microorganism of any one of claims 43 to
 49. 52. The recombinant enzyme of claim 51, wherein the enzyme has been subjected to a purification step.
 53. A crude fermentation product produced by culturing the comprising the genetically modified microorganism of any one of claims 43 to 49, wherein the crude fermentation product contains the at least one protein of claim
 24. 54. A multi-enzyme composition comprising enzymes produced by the genetically modified organism of any one of claims 43 to 50, and recovered therefrom.
 55. A multi-enzyme composition comprising at least one protein of claim 24, and at least one additional protein for degrading a lignocellulosic material or a fragment thereof that has biological activity.
 56. The multi-enzyme composition of claim 55, wherein the at least one additional protein for degrading a lignocellulosic material to fermentable sugars is selected from the group consisting of: SEQ ID NO:8, SEQ ID NO:14, SEQ ID NO:17, SEQ ID NO:20, SEQ ID NO:26 and SEQ ID NO:47, or a fragment thereof that has biological activity.
 57. The multi-enzyme composition of claim 55, wherein the composition comprises at least one cellobiohydrolase, at least one xylanase, at least one endoglucanase, at least one •-glucosidase, at least one •-xylosidase, and at least one accessory enzyme.
 58. The multi-enzyme composition of claim 55, wherein between about 50% and about 70% of the enzymes in the composition are cellobiohydrolases.
 59. The multi-enzyme composition of claim 55, wherein between about 10% and about 30% of the enzymes in the composition are xylanases.
 60. The multi-enzyme composition of claim 55, wherein between about 5% and about 15% of the enzymes in the composition are endoglucanases.
 61. The multi-enzyme composition of claim 55, wherein between about 1% and about 5% of the enzymes in the composition are •-glucosidases.
 62. The multi-enzyme composition of claim 55, wherein between about 1% and about 3% of the enzymes in the composition are •-xylosidases.
 63. The multi-enzyme composition of claim 55, wherein the composition comprises about 60% cellobiohydrolases, about 20% xylanases, about 10% endoglucanases, about 3% •-glucosidases, about 2% •-xylosidases, and about 5% accessory enzymes.
 64. The multi-enzyme composition of claim 57 or claim 63, wherein the xylanases are selected from the group consisting of: endoxylanases, exoxylanases, and •-xylosidases.
 65. The multi-enzyme composition of claim 57 or claim 63, wherein the accessory enzymes include an enzyme selected from the group consisting of: ligninase, glucuronidase, arabinofuranosidase, arabinogalactanase, furilic acid esterase, lipase, pectinase, glucomannase, amylase, laminarinase, xyloglucanase, galactanase, glucoamylase, pectate lyase, chitinase, exo-•-D-glucosaminidase, cellobiose dehydrogenase, and acetylxylan esterase.
 66. The multi-enzyme composition of claim 55, wherein the composition comprises at least one protein encoded by the nucleic acid molecule of claim 8, at least one protein encoded by the nucleic acid molecule of claim 9, at least one protein encoded by the nucleic acid molecule of claim 10 at least one protein encoded by the nucleic acid molecule of claim 11, and at least one protein encoded by the nucleic acid molecule of claim
 12. 67. The multi-enzyme composition of claim 55, wherein the composition comprises: a) at least one first protein comprising an amino acid sequence that is at least 95% identical to an amino acid sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8 and SEQ ID NO:11 and has cellobiohydrolase activity, or a fragment thereof that has cellobiohydrolase activity; b) at least one second protein comprising an amino acid sequence that is at least 95% identical to an amino acid sequence selected from the group consisting of: SEQ ID NO:14, SEQ ID NO:94, SEQ ID NO:17, SEQ ID NO:20 and SEQ ID NO:23 and has endoglucanase activity, or a fragment thereof that has endoglucanase activity; and c) at least one third protein comprising an amino acid sequence that is at least 95% identical to an amino acid sequence selected from the group consisting of: SEQ ID NO:26, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38 and SEQ ID NO:41 and has xylanase activity, or a fragment thereof that has xylanase activity.
 68. The multi-enzyme composition of claim 67, wherein the composition further comprises a fourth protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:44 and has β-glucosidase activity, or a fragment thereof that has β-glucosidase activity.
 69. The multi-enzyme composition of claim 68, wherein the composition further comprises at least one fifth protein comprising an amino acid sequence that is at least 95% identical to an amino acid sequence selected from the group consisting of: SEQ ID NO:47, SEQ ID NO:50, SEQ ID NO:53, SEQ ID NO:56, SEQ ID NO:59, SEQ ID NO:62, SEQ ID NO:65, SEQ ID NO:68, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:77, SEQ ID NO:80, SEQ ID NO:83, SEQ ID NO:86, SEQ ID NO:89, and SEQ ID NO:92, and has hemicellulase or chitinase activity, or a fragment thereof that has hemicellulase or chitinase activity
 70. A multi-enzyme composition comprising: a) a first protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:2 and has cellobiohydrolase activity, or a fragment thereof that has cellobiohydrolase activity; b) a second protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:8 and has cellobiohydrolase activity, or a fragment thereof that has cellobiohydrolase activity; c) a third protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:94 and has endoglucanase activity, or a fragment thereof that has endoglucanase activity; d) a fourth protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:29 and has xylanase activity, or a fragment thereof that has xylanase activity; and e) a fifth protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:44 and has β-glucosidase activity, or a fragment thereof that has β-glucosidase activity.
 71. The multi-enzyme composition of claim 70, further comprising a sixth protein that has β-xylosidase activity, or a fragment thereof that has β-xylosidase activity.
 72. The multi-enzyme composition of claim 70, further comprising one or more proteins selected from the group consisting of: d) a protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:5 and has cellobiohydrolase activity, or a fragment thereof that has cellobiohydrolase activity; e) a protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:20 and has endoglucanase activity, or a fragment thereof that has endoglucanase activity; f) a protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:26 and has xylanase activity, or a fragment thereof that has xylanase activity; and d) a protein comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:47 and has arabinogalactanase activity, or a fragment thereof that has arabinogalactanase activity.
 73. The multi-enzyme composition of any one of claims 54 to 72, wherein the multi-enzyme composition comprises at least one hemicellulase.
 74. The multi-enzyme composition of claim 73, wherein the hemicellulase is selected from the group consisting of a xylanase, an arabinofuranosidase, an acetyl xylan esterase, a glucuronidase, and endo-galactanase, a mannanase, an endo arabinase, an exo arabinase, an exo-galactanase, a ferulic acid esterase, a galactomannanase, a xylogluconase, and mixtures thereof.
 75. The multi-enzyme composition of claim 74, wherein the xylanase is selected from the group consisting of endoxylanases, exoxylanase, and β-xylosidase.
 76. The multi-enzyme composition of any one of claims 54 to 72, wherein the multi-enzyme composition comprises at least one cellulase.
 77. The multi-enzyme composition of any one of claims 54 to 72, wherein the composition is a crude fermentation product.
 78. The multi-enzyme composition of any one of claims 54 to 72, wherein the composition is a crude fermentation product that has been subjected to a purification step.
 79. The multi-enzyme composition of any one of claims 54 to 72, further comprising one or more accessory enzymes.
 80. The multi-enzyme composition of claim 79, wherein the accessory enzymes includes at least one enzyme selected from the group consisting of: cellulase, xylanase, ligninase, glucuronidase, arabinofuranosidase, arabinogalactanase, furilic acid esterase, lipase, pectinase, glucomannase, amylase, laminarinase, xyloglucanase, galactanase, glucoamylase, pectate lyase, chitinase, exo-•-D-glucosaminidase, cellobiose dehydrogenase, and acetylxylan esterase.
 81. The multi-enzyme composition of claim 79, wherein the accessory enzyme is selected from the group consisting of a glucoamylase, a pectinase, and a ligninase.
 82. The multi-enzyme composition of claim 79, wherein the accessory enzyme is a glucoamylase.
 83. The multi-enzyme composition of claim 79, wherein the accessory enzyme is added as a crude or a semi-purified enzyme mixture.
 84. The multi-enzyme composition of claim 79, wherein the accessory enzyme is produced by culturing at least one organism on a substrate to produce the enzyme.
 85. A method for degrading a lignocellulosic material to fermentable sugars, comprising contacting the lignocellulosic material with at least one isolated protein of claim
 24. 86. The method of claim 85, wherein the isolated protein is part of a multi-enzyme composition.
 87. A method for degrading a lignocellulosic material to fermentable sugars, comprising contacting the lignocellulosic material with at least one multi-enzyme composition of any one of claims 54 to
 84. 88. A method for producing an organic substance, comprising: a) saccharifying a lignocellulosic material with a multi-enzyme composition of any one of claims 54 to 84; b) fermenting the saccharified lignocellulosic material obtained with one or more fermentating microoganisms; and c) recovering the organic substance from the fermentation.
 89. The method of claim 88, wherein the steps of saccharifying and fermenting are performed simultaneously.
 90. The method of claim 88, wherein the organic substance is an alcohol, organic acid, ketone, amino acid, or gas.
 91. The method of claim 88, wherein the organic substance is an alcohol.
 92. The method of claim 91, wherein the alcohol is ethanol.
 93. The method of any one of claims 85 to 92, wherein the lignocellulosic material is selected from the group consisting of consisting of herbaceous material, agricultural residue, forestry residue, municipal solid waste, waste paper, and pulp and paper mill residue.
 94. The method of any one of claims 85 to 92, wherein the lignocellulosic material is distiller's dried grains or distiller's dried grains with solubles.
 95. The method of any one of claims 85 to 92, wherein the distiller's dried grains or distiller's dried grains with solubles is derived from corn.
 96. A method for degrading a lignocellulosic material consisting of distiller's dried grains or distiller's dried grains with solubles to sugars, the method comprising contacting the distiller's dried grains or distiller's dried grains with solubles with a multi-enzyme composition, whereby at least 10% of the fermentable sugars are liberated, wherein the multi-enzyme composition is the multi-enzyme composition of any one of claims 54 to
 84. 97. The method of claim 96, whereby at least 15% of the sugars are liberated.
 98. The method of claim 96, whereby at least 20% of the sugars are liberated.
 99. The method of claim 96, whereby at least 23% of the sugars are liberated.
 100. The method of claim 96, wherein the distiller's dried grains or distiller's dried grains with solubles is derived from corn.
 101. The method of any one of claims 85 to 100, further comprising a pretreatment process for pretreating the lignocellulosic material.
 102. The method of claim 101, wherein the pretreatment process is selected from the group consisting of physical treatment, metal ion, ultraviolet light, ozone, organosolv treatment, steam explosion treatment, lime impregnation with steam explosion treatment, hydrogen peroxide treatment, hydrogen peroxide/ozone (peroxone) treatment, acid treatment, dilute acid treatment, and base treatment.
 103. The method of claim 101, wherein the pretreatment process is selected from the group consisting of organosolv, steam explosion, heat treatment and AFEX.
 104. The method of claim 103, wherein the heat treatment comprises heating the lignocellulosic material to 121° C. for 15 minutes.
 105. The method of any one of claims 85 to 104, further comprising detoxifying the lignocellulosic material.
 106. The method of any one of claims 85 to 105, further comprising recovering the fermentable sugar.
 107. The method of claim 106, wherein the sugar is selected from the group consisting of glucose, xylose, arabinose, galactose, mannose, rhamnose, sucrose and fructose.
 108. The method of any one of claims 85 to 107, further comprising recovering the contacted lignocellulosic material after the fermentable sugars are degraded.
 109. A feed additive comprising the recovered lignocellulosic material of claim
 108. 110. The feed additive of claim 109, wherein the protein content of the recovered lignocellulosic material is higher than that of the starting lignocellulosic material.
 111. A method of improving the performance of an animal which comprises administering to the animal the feed additive of claim
 109. 112. A method for improving the nutritional quality of an animal feed comprising adding the feed additive of claim 109 to an animal feed.
 113. A method for stonewashing a fabric, comprising contacting the fabric with at least one isolated protein of claim
 24. 114. A method for stonewashing a fabric, comprising contacting the fabric with at least one multi-enzyme composition of any one of claims 54 to
 84. 115. The method of claim 113 or claim 114, wherein the fabric is denim.
 116. A method for enhanching the softness or feel of a fabric or depilling a fabric, comprising contacting the fabric with at least one isolated protein of claim 24 or a fragment of at least one isolated protein of claim 24 comprising a cellulose binding domain (CBD) of the protein.
 117. A method for enhanching the softness or feel of a fabric or depilling a fabric, comprising contacting the fabric with at least one multi-enzyme composition of any one of claims 54 to
 84. 118. A method for restoring color to or brightening a fabric, comprising contacting the fabric with at least one isolated protein of claim
 24. 119. A method for restoring color to or brightening a fabric, comprising contacting the fabric with at least one multi-enzyme composition of any one of claims 54 to
 84. 120. A method of biopolishing, defibrillating, bleaching, dyeing or desizing a fabric, comprising contacting the fabric with at least one isolated protein of claim
 24. 121. A method of biopolishing, defibrillating, bleaching, dyeing or desizing a fabric, comprising contacting the fabric with at least one multi-enzyme composition of any one of claims 54 to
 84. 122. A method of deinking or biobleaching paper or pulp, comprising contacting the paper or pulp with at least one isolated protein of claim
 24. 123. A method of deinking or biobleaching paper or pulp, comprising contacting the paper or pulp with at least one multi-enzyme composition of any one of claims 54 to
 84. 124. A method for enhancing the cleaning ability of a detergent composition, comprising adding at least one isolated protein of claim 24 to the detergent composition.
 125. A method for enhancing the cleaning ability of a detergent composition, comprising adding at least one multi-enzyme composition of any one of claims 54 to 84 to the detergent composition.
 126. A detergent composition, comprising at least one isolated protein of claim 24 and at least one surfactant.
 127. A detergent composition, comprising at least one multi-enzyme composition of any one of claims 54 to 84 and at least one surfactant.
 128. A method for inhibiting or reducing fungal growth, comprising contacting a fungus or an area susceptible to fungal growth with at least one isolated protein of claim
 25. 129. A method for reducing or preventing insect infestation on a plant, comprising contacting the plant with at least one isolated protein of claim
 25. 130. A method for reducing or preventing allergic inflammation or asthma, comprising administering at least one isolated protein of claim 25 to a subject.
 131. A lysing enzyme for the generation of protoplasts from fungi, comprising at least one isolated protein of claim
 25. 132. An insecticide composition, comprising at least one isolated protein of claim
 25. 